Genes and uses for plant improvement

ABSTRACT

Transgenic seed for crops with improved traits are provided by trait-improving recombinant DNA where plants grown from such transgenic seed exhibit one or more improved traits as compared to a control plant. Of particular interest are transgenic plants that have increased yield. The present invention also provides recombinant DNA molecules for expression of a protein, and recombinant DNA molecules for expression of mRNA complementary to at least a portion of an mRNA native to the target plant for use in gene suppression to suppress the expression of a protein.

CROSS REFERENCE TO RELATED APPLICATIONS

This application is a continuation of and claims the benefit of priority to U.S. patent application Ser. No. 11/087,099, filed Mar. 22, 2005, which claims benefit of U.S. provisional application Ser. No. 60/556,841, filed Mar. 25, 2004, which applications are incorporated herein by reference and made a part hereof in their entirety, and the benefit of priority of each of which is claimed herein.

INCORPORATION OF SEQUENCE LISTING

Two copies of the sequence listing (Copy 1 and Copy 2) and a computer readable form (CRF) of the sequence listing, all on CD-ROMs, each containing the file named 3126.001US2.txt, which is 34,279,424 bytes (measured in MS-WINDOWS) and was created on Jan. 24, 2014, are herein incorporated by reference.

FIELD OF THE INVENTION

Disclosed herein are inventions in the field of plant genetics and developmental biology. More specifically, the present invention provides transgenic seeds for crops, wherein the genome of said seed comprises recombinant DNA, the expression of which results in the production of transgenic plants that have improved trait(s).

BACKGROUND OF THE INVENTION

Transgenic plants with improved traits such as improved yield, environmental stress tolerance, pest resistance, herbicide tolerance, modified seed compositions, and the like are desired by both farmers and consumers. Although considerable efforts in plant breeding have provided significant gains in desired traits, the ability to introduce specific DNA into plant genomes provides further opportunities for generation of plants with improved and/or unique traits. The ability to develop transgenic plants with improved traits depends in part on the identification of genes that are useful in recombinant DNA constructs for production of transformed plants with improved properties.

SUMMARY OF THE INVENTION

This invention provides transgenic seeds, transgenic plants and DNA constructs with trait-improving recombinant DNA from a gene or homolog which has been demonstrated for trait improvement in a model plant. More specifically, such recombinant DNA is from a gene identified in a model plant screen as disclosed herein or homologues of such gene, e.g., from related species or in some cases from a broad range of unrelated species. In particular aspects of the invention the recombinant DNA will express a protein having an amino acid sequence with at least 90% identity to a consensus amino acid sequence in the group consisting of the consensus amino acid sequence of SEQ ID NO:240 and its homologs through SEQ ID NO:478 and its homologs, but excluding SEQ ID NO:391 and its homologs. The amino acid sequences of homologs are SEQ ID NO: 479 through SEQ ID NO: 12463. Tables 2 identifying the sequences of homologs for proteins encoded by the trait-improving genes described supra is provided herein as appendix. In some cases of trait improvement, the recombinant DNA encodes a protein; in other cases, the recombinant DNA suppresses endogenous protein expression. In a broad aspect this invention provides transgenic seed for growing crop plants with improved traits, such crop plants with improved traits and the plant parts including transgenic seed produced by such crop plants. The improved trait provided by the recombinant DNA in the transgenic crop plant of this invention is identified by comparison to a control plant, i.e., a plant without the trait-improving recombinant DNA. In one aspect of the invention, transgenic crop plant grown from the transgenic seed has improved yield, as compared to the yield of a control plant, e.g., a plant without the recombinant DNA that produces the increased yield. Increased yield may be characterized as plant yield increase under non-stress conditions, or by plant yield increase under one or more environmental stress conditions including, but not limited to, water deficit stress, cold stress, heat stress, high salinity stress, shade stress, and low nitrogen availability stress. Still another aspect of the present invention also provides transgenic plants having other improved phenotypes, such as improved plant development, plant morphology, plant physiology or seed composition as compared to a corresponding trait of a control plant. The various aspects of this invention are especially useful for transgenic seed and transgenic plants having improved traits in corn (also know as maize), soybean, cotton, canola (rape), wheat, sunflower, sorghum, alfalfa, barley, millet, rice, tobacco, fruit and vegetable crops, and turfgrass.

The invention also comprises recombinant DNA constructs. In one aspect such recombinant DNA constructs useful for the transgenic seed and transgenic plants of this invention comprise a promoter functional in a plant cell operably linked to a DNA segment for expressing a protein associated with a trait in a model plant or a homologue. In another aspect the recombinant DNA constructs useful for the transgenic seed and transgenic plants of this invention comprise a promoter functional in a plant cell operably linked to a DNA segment for suppressing the level of an endogenous plant protein which is a homologue to a model-plant protein, the suppression of which is associated with an improved trait. Suppression can be effected by any of a variety of methods known in the art, e.g., post transcriptional suppression by anti-sense, sense, dsRNA and the like or by transcriptional suppression.

This invention also provides a method of producing a transgenic crop plant having at least one improved trait, wherein the method comprises providing to a grower of transgenic seeds comprising recombinant DNA for expression or suppression of a trait-improving gene provided herein, and growing transgenic plant from said transgenic seed. Such methods can be used to generate transgenic crop plants having at least one improved traits under one or more environmental stress conditions including, but not limited to, water deficit stress, cold stress, heat stress, high salinity stress, shade stress, and low nitrogen availability stress. In another aspect, such method also can be used to generate transgenic crop plants having improved plant development, plant morphology, plant physiology or seed component phenotype as compared to a corresponding phenotype of a control plant. Of particular interest are uses of such methods to generate transgenic crop plants having increased yield under non-stress condition, or under one or more stress conditions.

One a particular embodiment of this invention provides transgenic seeds comprising trait improving recombinant DNA in its genome for the expression of a bacterial phytochrome protein. Transgenic plants resulting from such invention have improved tolerance to water deficit stress, cold stress and low nitrogen availability stress. In another aspect, transgenic crop plants overexpressing the bacterial phytochrome protein have increased yield under non-stress condition, or under one or more stress conditions.

DETAILED DESCRIPTION OF THE INVENTION

The present invention is directed to transgenic plant seed, wherein the genome of said transgenic plant seed comprises a trait-improving recombinant DNA as provided herein, and transgenic plant grown from such seed possesses an improved trait as compared to the trait of a control plant. In one aspect, the present invention relates to transgenic plants wherein the improved trait is one or more traits including improved drought stress tolerance, improved heat stress tolerance, improved cold stress tolerance, improved high salinity stress tolerance, improved low nitrogen availability stress tolerance, improved shade stress tolerance, improved plant growth and development at the stages of seed imbibition through early vegetative phase, and improved plant growth and development at the stages of leaf development, flower production and seed maturity. Of particular interest are the transgenic plants grown from transgenic seeds provided herein wherein the improved trait is increased seed yield. Recombinant DNA constructs disclosed by the present invention comprise recombinant polynucleotides providing for the production of mRNA to modulate gene expression, imparting improved traits to plants.

As used herein, “gene” refers to chromosomal DNA, plasmid DNA, cDNA, synthetic DNA, or other DNA that encodes a peptide, polypeptide, protein, or RNA molecule, and regions flanking the coding sequences involved in the regulation of expression.

As used herein, “transgenic seed” refers to a plant seed whose genome has been altered by the incorporation of recombinant DNA, e.g., by transformation as described herein. The term “transgenic plant” is used to refer to the plant produced from an original transformation event, or progeny from later generations or crosses of a plant to a transformed plant, so long as the progeny contains the recombinant DNA in its genome. As used herein, “recombinant DNA” refers to a polynucleotide having a genetically engineered modification introduced through combination of endogenous and/or exogenous elements in a transcription unit, manipulation via mutagenesis, restriction enzymes, and the like or simply by inserting multiple copies of a native transcription unit. Recombinant DNA may comprise DNA segments obtained from different sources, or DNA segments obtained from the same source, but which have been manipulated to join DNA segments which do not naturally exist in the joined form. A recombinant polynucleotide may exist outside of the cell, for example as a PCR fragment, or integrated into a genome, such as a plant genome.

As used herein, “trait” refers to a physiological, morphological, biochemical, or physical characteristic of a plant or particular plant material or cell. In some instances, this characteristic is visible to the human eye, such as seed or plant size, or can be measured by biochemical techniques, such as detecting the protein, starch, or oil content of seed or leaves, or by observation of a metabolic or physiological process, e.g., by measuring uptake of carbon dioxide, or by the observation of the expression level of a gene or genes, e.g., by employing Northern analysis, RT-PCR, microarray gene expression assays, or reporter gene expression systems, or by agricultural observations such as stress tolerance, yield, or pathogen tolerance.

As used herein, “control plant” is a plant without trait-improving recombinant DNA. A control plant is used to measure and compare trait improvement in a transgenic plant with such trait-improving recombinant DNA. A suitable control plant may be a non-transgenic plant of the parental line used to generate a transgenic plant herein. Alternatively, control plant may be a transgenic plant that comprises an empty vector or marker gene, but does not contain the recombinant DNA that produces the trait improvement. A control plant may also be a negative segregant progeny of hemizygous transgenic plant. In certain demonstrations of trait improvement, the use of a limited number of control plants can cause a wide variation in the control dataset. To minimize the effect of the variation within the control dataset, a “reference” is used. As use herein a “reference” is a trimmed mean of all data from both transgenic and control plants grown under the same conditions and at the same developmental stage. The trimmed mean is calculated by eliminating a specific percentage, i.e., 20%, of the smallest and largest observation from the data set and then calculating the average of the remaining observation.

As used herein, “trait improvement” refers to a detectable and desirable difference in a characteristic in a transgenic plant relative to a control plant or a reference. In some cases, the trait improvement can be measured quantitatively. For example, the trait improvement can entail at least a 2% desirable difference in an observed trait, at least a 5% desirable difference, at least about a 10% desirable difference, at least about a 20% desirable difference, at least about a 30% desirable difference, at least about a 50% desirable difference, at least about a 70% desirable difference, or at least about a 100% difference, or an even greater desirable difference. In other cases, the trait improvement is only measured qualitatively. It is known that there can be a natural variation in a trait. Therefore, the trait improvement observed entails a change of the normal distribution of the trait in the transgenic plant compared with the trait distribution observed in a control plant or a reference, which is evaluated by statistical methods provided herein. Trait improvement includes, but not limited to, yield increase, including increased yield under non-stress conditions and increased yield under environmental stress conditions. Stress conditions may include, for example, drought, shade, fungal disease, viral disease, bacterial disease, insect infestation, nematode infestation, cold temperature exposure, heat exposure, osmotic stress, reduced nitrogen nutrient availability, reduced phosphorus nutrient availability and high plant density. Many agronomic traits can affect “yield”, including without limitation, plant height, pod number, pod position on the plant, number of internodes, incidence of pod shatter, grain size, efficiency of nodulation and nitrogen fixation, efficiency of nutrient assimilation, resistance to biotic and abiotic stress, carbon assimilation, plant architecture, resistance to lodging, percent seed germination, seedling vigor, and juvenile traits. Other traits that can affect yield include, efficiency of germination (including germination in stressed conditions), growth rate (including growth rate in stressed conditions), ear number, seed number per ear, seed size, composition of seed (starch, oil, protein) and characteristics of seed fill. Also of interest is the generation of transgenic plants that demonstrate desirable phenotypic properties that may or may not confer an increase in overall plant yield. Such properties include improved plant morphology, plant physiology or improved components of the mature seed harvested from the transgenic plant.

As used herein, “yield-limiting environment” refers to the condition under which a plant would have the limitation on yield including environmental stress conditions.

As used herein, “stress condition” refers to the condition unfavorable for a plant, which adversely affect plant metabolism, growth and/or development. A plant under the stress condition typically shows reduced germination rate, retarded growth and development, reduced photosynthesis rate, and eventually leading to reduction in yield.

Specifically, “water deficit stress” used herein preferably refers to the sub-optimal conditions for water and humidity needed for normal growth of natural plants. Relative water content (RWC) can be used as a physiological measure of plant water deficit. It measures the effect of osmotic adjustment in plant water status, when a plant is under stressed conditions. Conditions which may result in water deficit stress include heat, drought, high salinity and PEG induced osmotic stress.

“Cold stress” used herein preferably refers to the exposure of a plant to a temperatures below (two or more degrees Celsius below) those normal for a particular species or particular strain of plant.

As used herein, “sufficient nitrogen growth condition” refers to the growth condition where the soil or growth medium contains or receives enough amounts of nitrogen nutrient to sustain a healthy plant growth and/or for a plant to reach its typical yield for a particular plant species or a particular strain. As used herein, “nitrogen nutrient” means any one or any mix of the nitrate salts commonly used as plant nitrogen fertilizer, including, but not limited to, potassium nitrate, calcium nitrate, sodium nitrate, ammonium nitrate. The term ammonium as used herein means any one or any mix of the ammonium salts commonly used as plant nitrogen fertilizer, e.g., ammonium nitrate, ammonium chloride, ammonium sulfate, etc. One skilled in the art would recognize what constitute such soil, media and fertilizer inputs for most plant species. “Low nitrogen availability stress” used herein refers to a plant growth condition that does not contain sufficient nitrogen nutrient to maintain a healthy plant growth and/or for a plant to reach its typical yield under a sufficient nitrogen growth condition, and preferably refers to a growth condition with 50% or less of the conventional nitrogen inputs.

“Shade stress” used herein preferably refers to limited light availability that triggers the shade avoidance response in plant. Plants are subject to shade stress when localized at lower part of the canopy, or in close proximity of neighboring vegetation. Shade stress may become exacerbated when the planting density exceeds the average prevailing density for a particular plant species. The average prevailing densities per acre of a few other examples of crop plants in the USA in the year 2000 were: wheat 1,000,000-1,500,000; rice 650,000-900,000; soybean 150,000-200,000, canola 260,000-350,000, sunflower 17,000-23,000 and cotton 28,000-55,000 plants per acre (Cheikh, et al., (2003) U.S. Patent Application No. 20030101479).

As used herein, “increased yield” of a transgenic plant of the present invention may be evidenced and measured in a number of ways, including test weight, seed number per plant, seed weight, seed number per unit area (i.e., seeds, or weight of seeds, per acre), bushels per acre, tons per acre, tons per acre, kilo per hectare. For example, maize yield may be measured as production of shelled corn kernels per unit of production area, e.g., in bushels per acre or metric tons per hectare, often reported on a moisture adjusted basis, e.g., at 15.5% moisture. Increased yield may result from improved utilization of key biochemical compounds, such as nitrogen, phosphorous and carbohydrate, or from improved responses to environmental stresses, such as cold, heat, drought, salt, and attack by pests or pathogens. Trait-improving recombinant DNA may also be used to provide transgenic plants having improved growth and development, and ultimately increased yield, as the result of modified expression of plant growth regulators or modification of cell cycle or photosynthesis pathways.

As used herein, “expression” refers to transcription of DNA to produce RNA. The resulting RNA may be without limitation mRNA encoding a protein, antisense RNA that is complementary to an mRNA encoding a protein, or an RNA transcript comprising a combination of sense and antisense gene regions, such as for use in RNAi technology. Expression as used herein may also refer to production of encoded protein from mRNA.

As used herein, “promoter” includes reference to a region of DNA upstream from the start of transcription and involved in recognition and binding of RNA polymerase and other proteins to initiate transcription. A “plant promoter” is a promoter capable of initiating transcription in plant cells whether or not its origin is a plant cell. Exemplary plant promoters include, but are not limited to, those that are obtained from plants, plant viruses, and bacteria which comprise genes expressed in plant cells such as Agrobacterium or Rhizobium. Examples of promoters under developmental control include promoters that preferentially initiate transcription in certain tissues, such as leaves, roots, or seeds. Such promoters are referred to as “tissue preferred”. Promoters which initiate transcription only in certain tissues are referred to as “tissue specific”. A “cell type” specific promoter primarily drives expression in certain cell types in one or more organs, for example, vascular cells in roots or leaves. An “inducible” or “repressible” promoter is a promoter which is under environmental control. Examples of environmental conditions that may effect transcription by inducible promoters include anaerobic conditions, or certain chemicals, or the presence of light. Tissue specific, tissue preferred, cell type specific, and inducible promoters constitute the class of “non-constitutive” promoters. A “constitutive” promoter is a promoter which is active under most conditions. As used herein, “antisense orientation” includes reference to a polynucleotide sequence that is operably linked to a promoter in an orientation where the antisense strand is transcribed. The antisense strand is sufficiently complementary to an endogenous transcription product such that translation of the endogenous transcription product is often inhibited.

As used herein, “operably linked” refers to the association of two or more nucleic acid fragments on a single nucleic acid fragment so that the function of one is affected by the other. For example, a promoter is operably linked with a coding sequence when it is capable of affecting the expression of that coding sequence (i.e., that the coding sequence is under the transcriptional control of the promoter). Coding sequences can be operably linked to regulatory sequences in sense or antisense orientation.

As used herein, “consensus sequence” refers to an artificial, amino acid sequence of conserved parts of the proteins encoded by homologous genes, e.g., as determined by a CLUSTALW alignment of amino acid sequence of homolog proteins.

As used herein, “homolog” refers to a gene related to a second gene by descent from a common ancestral DNA sequence. The term, homolog, may apply to the relationship between genes separated by the event of speciation (see ortholog) or to the relationship between genes separated by the event of genetic duplication (see paralog). Homologs can be from the same or a different organism that performs the same biological function. “Orthologs” refer to a set of homologous genes in different species that evolved from a common ancestral gene by specification. Normally, orthologs retain the same function in the course of evolution; and “paralogs” refer to a set of homologous genes in the same species that have diverged from each other as a consequence of genetic duplication.

Percent identity refers to the extent to which two optimally aligned DNA or protein segments are invariant throughout a window of alignment of components, e.g., nucleotide sequence or amino acid sequence. An “identity fraction” for aligned segments of a test sequence and a reference sequence is the number of identical components which are shared by sequences of the two aligned segments divided by the total number of sequence components in the reference segment over a window of alignment which is the smaller of the full test sequence or the full reference sequence. “Percent identity” (“% identity”) is the identity fraction times 100. “% identity to a consensus amino acid sequence” is 100 times the identity fraction in a window of alignment of an amino acid sequence of a test protein optimally aligned to consensus amino acid sequence of this invention.

As used herein “Arabidopsis” means plants of Arabidopsis thaliana.

Recombinant DNA Constructs

The present invention provides recombinant DNA constructs comprising one or more polynucleotides disclosed herein for imparting one or more improved traits to transgenic plant. Such constructs also typically comprise a promoter operatively linked to said polynucleotide to provide for expression in a target plant. Other construct components may include additional regulatory elements, such as 5′ or 3′ untranslated regions (such as polyadenylation sites), intron regions, and transit or signal peptides. Such recombinant DNA constructs can be assembled using methods known to those of ordinary skill in the art.

In a preferred embodiment, a polynucleotide of the present invention is operatively linked in a recombinant DNA construct to a promoter functional in a plant to provide for expression of the polynucleotide in the sense orientation such that a desired polypeptide is produced. Also provided are embodiments wherein a polynucleotide is operatively linked to a promoter functional in a plant to provide for expression of the polynucleotide in the antisense orientation such that a complementary copy of at least a portion of an mRNA native to the target plant host is produced.

Recombinant constructs prepared in accordance with the present invention may also generally include a 3′ untranslated DNA region (UTR) that typically contains a polyadenylation sequence following the polynucleotide coding region. Examples of useful 3′ UTRs include those from the nopaline synthase gene of Agrobacterium tumefaciens (nos), a gene encoding the small subunit of a ribulose-1,5-bisphosphate carboxylase-oxygenase (rbcS), and the T7 transcript of Agrobacterium tumefaciens. Constructs and vectors may also include a transit peptide for targeting of a gene target to a plant organelle, particularly to a chloroplast, leucoplast or other plastid organelle. For descriptions of the use of chloroplast transit peptides, see U.S. Pat. No. 5,188,642 and U.S. Pat. No. 5,728,925, incorporated herein by reference.

Table1 provides a list of genes that can provide recombinant DNA that was used in a model plant to discover associate improved traits and that can be used with homologs to define a consensus amino acid sequence for characterizing recombinant DNA in the transgenic seeds, transgenic plants, DNA constructs and methods of this invention. “NUC SEQ ID NO” refers to a SEQ ID NO. for a particular DNA sequence in the Sequence Listing. “PEP SEQ ID NO” refers to a SEQ ID NO. in the Sequence Listing for the amino acid sequence of a protein cognate to a particular DNA “construct_id” refers to an arbitrary number used to identify a particular recombinant DNA construct comprising the particular DNA. “gene” refers to an arbitrary name used to identify the particular DNA. “orientation” refers to the orientation of the particular DNA in a recombinant DNA construct relative to the promoter. “species” refers to the organism from which the particular DNA was derived.

TABLE 1 Nuc SEQ ID Pep SEQ ID construct_id Gene orientation Species 1 240 19867 CGPG4046 Sense Glycine max 2 241 74518 CGPG6792 Sense Pseudomonas fluorescens PfO-1 3 242 15816 CGPG2244 Sense Arabidopsis thaliana 4 243 17918 CGPG2774 Sense Arabidopsis thaliana 5 244 15306 CGPG1909 AntiSense Arabidopsis thaliana 6 245 12038 CGPG1087 Sense Arabidopsis thaliana 7 246 12046 CGPG1106 Sense Arabidopsis thaliana 8 247 13432 CGPG1525 Sense Arabidopsis thaliana 9 248 13711 CGPG1114 Sense Arabidopsis thaliana 10 249 14809 CGPG692 Sense Arabidopsis thaliana 11 250 14951 CGPG1636 Sense Arabidopsis thaliana 12 251 15632 CGPG1469 Sense Arabidopsis thaliana 13 252 16147 CGPG2088 Sense Arabidopsis thaliana 14 253 16158 CGPG2169 Sense Arabidopsis thaliana 15 254 16170 CGPG2192 Sense Arabidopsis thaliana 16 255 16171 CGPG2194 Sense Arabidopsis thaliana 17 256 16175 CGPG2204 Sense Arabidopsis thaliana 18 257 17430 CGPG2478 Sense Arabidopsis thaliana 19 258 17819 CGPG2587 Sense Arabidopsis thaliana 20 259 17921 CGPG2878 Sense Arabidopsis thaliana 21 260 17928 CGPG2739 Sense Arabidopsis thaliana 22 261 18637 CGPG3450 Sense Arabidopsis thaliana 23 262 18816 CGPG2406 Sense Arabidopsis thaliana 24 263 19227 CGPG3025 Sense Arabidopsis thaliana 25 264 19429 CGPG3486 Sense Arabidopsis thaliana 26 265 70235 CGPG96 Sense Arabidopsis thaliana 27 266 72634 CGPG4855 Sense Arabidopsis thaliana 28 267 72752 CGPG5532 Sense Saccharomyces cerevisiae 29 268 12007 CGPG1089 AntiSense Arabidopsis thaliana 30 269 12290 CGPG977 AntiSense Arabidopsis thaliana 31 270 12343 CGPG581 AntiSense Arabidopsis thaliana 32 271 14348 CGPG1692 AntiSense Arabidopsis thaliana 33 272 15708 CGPG2167 AntiSense Arabidopsis thaliana 34 273 17615 CGPG2458 Anti-Sense Arabidopsis thaliana 35 274 17622 CGPG2454 Anti-Sense Arabidopsis thaliana 36 275 70714 CGPG1480 Anti-sense Arabidopsis thaliana 37 276 17925 CGPG2883 Sense Arabidopsis thaliana 38 277 18541 CGPG2971 Sense Arabidopsis thaliana 39 278 11425 CGPG628 Sense Arabidopsis thaliana 40 279 12263 CGPG799 Sense Arabidopsis thaliana 41 280 12288 CGPG811 Sense Arabidopsis thaliana 42 281 12910 CGPG985 Sense Arabidopsis thaliana 43 282 14335 CGPG1685 Sense Arabidopsis thaliana 44 283 17427 CGPG2475 Sense Arabidopsis thaliana 45 284 19140 CGPG1758 Sense Arabidopsis thaliana 46 285 19179 CGPG740 Sense Arabidopsis thaliana 47 286 19251 CGPG3118 Sense Arabidopsis thaliana 48 287 19443 CGPG2834 Sense Arabidopsis thaliana 49 288 19607 CGPG3397 Sense Arabidopsis thaliana 50 289 19915 CGPG4072 Sense Glycine max 51 290 70222 CGPG28 Sense Arabidopsis thaliana 52 291 70464 CGPG3773 Sense Arabidopsis thaliana 53 292 70474 CGPG3806 Sense Arabidopsis thaliana 54 293 70484 CGPG3853 Sense Arabidopsis thaliana 55 294 72474 CGPG4667 Sense Glycine max 56 295 13047 CGPG1324 ANTI-SENSE Arabidopsis thaliana 57 296 13304 CGPG1282 ANTI-SENSE Arabidopsis thaliana 58 297 13474 CGPG1600 ANTI-SENSE Arabidopsis thaliana 59 298 19252 CGPG3121 SENSE Arabidopsis thaliana 60 299 12612 CGPG1181 SENSE Arabidopsis thaliana 61 300 12926 CGPG1299 SENSE Arabidopsis thaliana 62 301 13230 CGPG1276 SENSE Arabidopsis thaliana 63 302 14235 CGPG1665 SENSE Arabidopsis thaliana 64 303 17305 CGPG2261 SENSE Arabidopsis thaliana 65 304 17470 CGPG2606 SENSE Arabidopsis thaliana 66 305 17718 CGPG1791 SENSE Arabidopsis thaliana 67 306 17904 CGPG1912 SENSE Arabidopsis thaliana 68 307 18280 CGPG3547 SENSE Arabidopsis thaliana 69 308 18287 CGPG3563 SENSE Arabidopsis thaliana 70 309 18501 CGPG2237 SENSE Arabidopsis thaliana 71 310 18877 CGPG3097 SENSE Arabidopsis thaliana 72 311 19531 CGPG3028 SENSE Arabidopsis thaliana 73 312 70405 CGPG1672 SENSE Arabidopsis thaliana 74 313 72136 CGPG5320 SENSE Glycine max 75 314 72611 CGPG4812 SENSE Arabidopsis thaliana 76 315 12627 CGPG1003 SENSE Arabidopsis thaliana 77 316 12813 CGPG825 SENSE Arabidopsis thaliana 78 317 14945 CGPG1776 SENSE Arabidopsis thaliana 79 318 15345 CGPG1504 SENSE Arabidopsis thaliana 80 319 15348 CGPG1514 SENSE Arabidopsis thaliana 81 320 16325 CGPG2195 SENSE Arabidopsis thaliana 82 321 16702 CGPG531 SENSE Arabidopsis thaliana 83 322 16836 CGPG2283 SENSE Arabidopsis thaliana 84 323 17002 CGPG1926 SENSE Arabidopsis thaliana 85 324 17012 CGPG2073 SENSE Arabidopsis thaliana 86 325 17017 CGPG1722 SENSE Arabidopsis thaliana 87 326 17344 CGPG2404 SENSE Arabidopsis thaliana 88 327 17426 CGPG2474 SENSE Arabidopsis thaliana 89 328 17655 CGPG2899 SENSE Arabidopsis thaliana 90 329 17656 CGPG2714 SENSE Arabidopsis thaliana 91 330 17906 CGPG2145 SENSE Arabidopsis thaliana 92 331 18278 CGPG3544 SENSE Arabidopsis thaliana 93 332 18822 CGPG2398 SENSE Arabidopsis thaliana 94 333 18881 CGPG3126 SENSE Arabidopsis thaliana 95 334 19213 CGPG3622 SENSE Arabidopsis thaliana 96 335 19239 CGPG3197 SENSE Arabidopsis thaliana 97 336 19247 CGPG3112 SENSE Arabidopsis thaliana 98 337 19460 CGPG2824 SENSE Arabidopsis thaliana 99 338 19512 CGPG2898 SENSE Arabidopsis thaliana 100 339 19533 CGPG3032 SENSE Arabidopsis thaliana 101 340 19603 CGPG3385 SENSE Arabidopsis thaliana 102 341 72126 CGPG5310 SENSE Glycine max 103 342 72437 CGPG5068 SENSE Arabidopsis thaliana 104 343 72441 CGPG5079 SENSE Arabidopsis thaliana 105 344 72639 CGPG4861 SENSE Arabidopsis thaliana 106 345 14825 CGPG1883 Anti-Sense Arabidopsis thaliana 107 346 17931 CGPG2890 Sense Arabidopsis thaliana 108 347 18854 CGPG3524 Sense Arabidopsis thaliana 109 348 12237 CGPG1206 Sense Arabidopsis thaliana 110 349 13414 CGPG1246 Sense Arabidopsis thaliana 111 350 16160 CGPG2172 Sense Arabidopsis thaliana 112 351 16226 CGPG1980 Sense Arabidopsis thaliana 113 352 16803 CGPG2179 Sense Arabidopsis thaliana 114 353 18260 CGPG3373 Sense Arabidopsis thaliana 115 354 18642 CGPG3230 Sense Arabidopsis thaliana 116 355 18721 CGPG3618 Sense Arabidopsis thaliana 117 356 19254 CGPG3123 Sense Arabidopsis thaliana 118 357 70247 CGPG34 Sense Arabidopsis thaliana 119 358 70650 CGPG4337 Sense Arabidopsis thaliana 120 359 11787 CGPG951 ANTI-SENSE Arabidopsis thaliana 120 359 12635 CGPG951 Sense Arabidopsis thaliana 121 360 13641 CGPG1211 ANTI-SENSE Arabidopsis thaliana 122 361 14515 CGPG1115 ANTI-SENSE Arabidopsis thaliana 123 362 14920 CGPG2027 ANTI-SENSE Arabidopsis thaliana 124 363 15204 CGPG2000 ANTI-SENSE Arabidopsis thaliana 125 364 15216 CGPG1906 ANTI-SENSE Arabidopsis thaliana 125 364 19058 CGPG1906 SENSE Arabidopsis thaliana 126 365 15330 CGPG1237 ANTI-SENSE Arabidopsis thaliana 127 366 19610 CGPG3419 SENSE Arabidopsis thaliana 128 367 14338 CGPG1706 SENSE Arabidopsis thaliana 129 368 17809 CGPG2436 SENSE Arabidopsis thaliana 130 369 72471 CGPG4648 SENSE Glycine max 131 370 16403 CGPG1983 SENSE Arabidopsis thaliana 132 371 17737 CGPG2623 SENSE Arabidopsis thaliana 133 372 18395 CGPG2994 SENSE Arabidopsis thaliana 134 373 72772 CGPG2418 SENSE Arabidopsis thaliana 135 374 19441 CGPG2783 SENSE Arabidopsis thaliana 136 375 11409 CGPG136 SENSE Arabidopsis thaliana 137 376 10486 CGPG137 SENSE Arabidopsis thaliana 138 377 12104 CGPG693 SENSE Arabidopsis thaliana 139 378 12258 CGPG836 SENSE Arabidopsis thaliana 140 379 12909 CGPG1195 SENSE Arabidopsis thaliana 141 380 14310 CGPG1037 SENSE Arabidopsis thaliana 142 381 14317 CGPG1150 SENSE Arabidopsis thaliana 143 382 14709 CGPG990 SENSE Arabidopsis thaliana 144 383 15123 CGPG1730 SENSE Arabidopsis thaliana 145 384 16013 CGPG978 SENSE Arabidopsis thaliana 146 385 16185 CGPG2025 SENSE Arabidopsis thaliana 147 386 16719 CGPG1817 SENSE Arabidopsis thaliana 148 387 17490 CGPG2638 SENSE Arabidopsis thaliana 149 388 17905 CGPG2101 SENSE Arabidopsis thaliana 150 389 18385 CGPG3609 SENSE Arabidopsis thaliana 151 390 18392 CGPG2989 SENSE Arabidopsis thaliana 153 392 18531 CGPG3215 SENSE Arabidopsis thaliana 154 393 18603 CGPG3423 SENSE Arabidopsis thaliana 155 394 19530 CGPG3026 SENSE Arabidopsis thaliana 156 395 70202 CGPG3949 SENSE Glycine max 157 396 72009 CGPG5273 SENSE Saccharomyces cerevisiae 158 397 72119 CGPG5332 SENSE Glycine max 159 398 10188 CGPG147 Anti-sense Arabidopsis thaliana 160 399 10404 CGPG25 Anti-Sense Arabidopsis thaliana 161 400 11333 CGPG583 Anti-Sense Arabidopsis thaliana 162 401 11719 CGPG710 Anti-Sense Arabidopsis thaliana 163 402 13663 CGPG1241 Anti-sense Arabidopsis thaliana 164 403 13958 CGPG1711 Anti-Sense Arabidopsis thaliana 165 404 15214 CGPG1904 Anti-Sense Arabidopsis thaliana 166 405 10483 CGPG447 Sense Arabidopsis thaliana 167 406 11711 CGPG466 Sense Arabidopsis thaliana 168 407 11909 CGPG471 Sense Arabidopsis thaliana 169 408 12216 CGPG1091 Sense Arabidopsis thaliana 170 409 12236 CGPG1193 Sense Arabidopsis thaliana 171 410 12256 CGPG824 Sense Arabidopsis thaliana 172 411 12806 CGPG714 Sense Arabidopsis thaliana 173 412 12904 CGPG204 Sense Arabidopsis thaliana 174 413 13212 CGPG1384 Sense Arabidopsis thaliana 175 414 13232 CGPG1281 Sense Arabidopsis thaliana 176 415 13912 CGPG1283 Sense Arabidopsis thaliana 177 416 14327 CGPG1606 Sense Arabidopsis thaliana 178 417 14704 CGPG1066 Sense Arabidopsis thaliana 179 418 14714 CGPG1431 Sense Arabidopsis thaliana 180 419 15142 CGPG1917 Sense Arabidopsis thaliana 181 420 17450 CGPG2684 Sense Arabidopsis thaliana 182 421 18607 CGPG3496 Sense Arabidopsis thaliana 183 422 19409 CGPG2691 Sense Arabidopsis thaliana 184 423 19412 CGPG2727 Sense Arabidopsis thaliana 185 424 13005 CGPG724 ANTI-SENSE Arabidopsis thaliana 186 425 10203 CGPG272 ANTI-SENSE Arabidopsis thaliana 187 426 11327 CGPG551 ANTI-SENSE Arabidopsis thaliana 188 427 11814 CGPG1041 ANTI-SENSE Arabidopsis thaliana 188 427 12018 CGPG1041 SENSE Arabidopsis thaliana 189 428 13003 CGPG673 ANTI-SENSE Arabidopsis thaliana 190 429 13949 CGPG1686 ANTI-SENSE Arabidopsis thaliana 191 430 16416 CGPG2258 ANTI-SENSE Arabidopsis thaliana 192 431 16438 CGPG1847 ANTI-SENSE Arabidopsis thaliana 193 432 17124 CGPG2432 ANTI-SENSE Arabidopsis thaliana 194 433 19132 CGPG1755 ANTI-SENSE Arabidopsis thaliana 195 434 17922 CGPG2880 SENSE Arabidopsis thaliana 196 435 19719 CGPG4171 SENSE Glycine max 197 436 17336 CGPG1732 SENSE Arabidopsis thaliana 197 436 14274 CGPG1732 ANTI-SENSE Arabidopsis thaliana 198 437 17735 CGPG2423 SENSE Arabidopsis thaliana 199 438 19249 CGPG3115 SENSE Arabidopsis thaliana 200 439 18513 CGPG3485 SENSE Arabidopsis thaliana 201 440 11517 CGPG224 SENSE Arabidopsis thaliana 202 441 12363 CGPG981 SENSE Arabidopsis thaliana 203 442 12922 CGPG1294 SENSE Arabidopsis thaliana 204 443 15360 CGPG1719 SENSE Arabidopsis thaliana 205 444 16028 CGPG2047 SENSE Arabidopsis thaliana 206 445 16648 CGPG2504 SENSE Agrobacterium tumefaciens 207 446 16705 CGPG1005 SENSE Arabidopsis thaliana 208 447 16715 CGPG2273 SENSE Arabidopsis thaliana 209 448 17316 CGPG2146 SENSE Arabidopsis thaliana 210 449 17331 CGPG1708 SENSE Arabidopsis thaliana 211 450 17339 CGPG2461 SENSE Arabidopsis thaliana 212 451 17420 CGPG2465 SENSE Arabidopsis thaliana 213 452 17446 CGPG2728 SENSE Arabidopsis thaliana 214 453 17487 CGPG2633 SENSE Arabidopsis thaliana 215 454 17740 CGPG2605 SENSE Arabidopsis thaliana 216 455 17752 CGPG2831 SENSE Arabidopsis thaliana 217 456 18021 CGPG685 SENSE Arabidopsis thaliana 218 457 18245 CGPG3343 SENSE Arabidopsis thaliana 219 458 18617 CGPG3521 SENSE Arabidopsis thaliana 220 459 18734 CGPG3198 SENSE Arabidopsis thaliana 221 460 18823 CGPG2830 SENSE Arabidopsis thaliana 222 461 19222 CGPG3017 SENSE Arabidopsis thaliana 223 462 19430 CGPG3487 SENSE Arabidopsis thaliana 224 463 12332 CGPG356 AntiSense Arabidopsis thaliana 225 464 13649 CGPG1544 Anti-Sense Arabidopsis thaliana 226 465 16113 CGPG2128 AntiSense Arabidopsis thaliana 227 466 12069 CGPG1188 Sense Arabidopsis thaliana 228 467 12906 CGPG313 Sense Arabidopsis thaliana 229 468 13443 CGPG1233 Sense Arabidopsis thaliana 230 469 14707 CGPG1141 Sense Arabidopsis thaliana 231 470 15116 CGPG1509 Sense Arabidopsis thaliana 232 471 16117 CGPG2234 Sense Arabidopsis thaliana 233 472 16136 CGPG2144 Sense Arabidopsis thaliana 234 473 19077 CGPG1808 Sense Arabidopsis thaliana 235 474 19178 CGPG3683 Sense Saccharomyces cerevisiae 236 475 70752 CGPG4465 Sense Arabidopsis thaliana 237 476 70753 CGPG4469 Sense Arabidopsis thaliana 238 477 70809 CGPG388 Sense Arabidopsis thaliana 239 478 72091 CGPG5264 Sense Saccharomyces cerevisiae

Recombinant DNA

Exemplary DNA for use in the present invention to improve traits in plants are provided herein as SEQ ID NO:1 through SEQ ID NO: 151 and SEQ ID NO: 153 through SEQ ID NO: 239. A subset of the exemplary DNA includes fragments of the disclosed full polynucleotides consisting of oligonucleotides of at least 15, preferably at least 16 or 17, more preferably at least 18 or 19, and even more preferably at least 20 or more, consecutive nucleotides. Such oligonucleotides are fragments of the larger molecules having a sequence selected from the group consisting of SEQ ID NO: 1 through SEQ ID NO: 151 and SEQ ID NO: 153 through SEQ ID NO: 239, and find use, for example as probes and primers for detection of the polynucleotides of the present invention.

Also of interest in the present invention are variants of the DNA provided herein. Such variants may be naturally occurring, including DNA from homologous genes from the same or a different species, or may be non-natural variants, for example DNA synthesized using chemical synthesis methods, or generated using recombinant DNA techniques. Degeneracy of the genetic code provides the possibility to substitute at least one base of the protein encoding sequence of a gene with a different base without causing the amino acid sequence of the polypeptide produced from the gene to be changed. Hence, a DNA useful in the present invention may have any base sequence that has been changed from the sequences provided herein by substitution in accordance with degeneracy of the genetic code.

Homologs of the genes providing DNA of demonstrated as useful in improving traits in model plants disclosed herein will generally demonstrate significant identity with the DNA provided herein. DNA is substantially identical to a reference DNA if, when the sequences of the polynucleotides are optimally aligned there is about 60% nucleotide equivalence; more preferably 70%; more preferably 80% equivalence; more preferably 85% equivalence; more preferably 90%; more preferably 95%; and/or more preferably 98% or 99% equivalence over a comparison window. A comparison window is preferably at least 50-100 nucleotides, and more preferably is the entire length of the polynucleotide provided herein. Optimal alignment of sequences for aligning a comparison window may be conducted by algorithms; preferably by computerized implementations of these algorithms (for example, the Wisconsin Genetics Software Package Release 7.0-10.0, Genetics Computer Group, 575 Science Dr., Madison, Wis.). The reference polynucleotide may be a full-length molecule or a portion of a longer molecule. Preferentially, the window of comparison for determining polynucleotide identity of protein encoding sequences is the entire coding region.

Recombinant DNA

Proteins useful for imparting improved traits are entire proteins or at least a sufficient portion of the entire protein to impart the relevant biological activity of the protein. The term “protein” also includes molecules consisting of one or more polypeptide chains. Thus, a protein useful in the present invention may constitute an entire protein having the desired biological activity, or may constitute a portion of an oligomeric protein having multiple polypeptide chains. Proteins useful for generation of transgenic plants having improved traits include the proteins with an amino acid sequence provided herein as SEQ ID NO: 240 through SEQ ID NO: 390 and SEQ ID NO: 392 through SEQ ID NO: 478, as well as homologs of such proteins.

Homologs of the proteins useful in the present invention may be identified by comparison of the amino acid sequence of the protein to amino acid sequences of proteins from the same or different plant sources, e.g., manually or by using known homology-based search algorithms such as those commonly known and referred to as BLAST, FASTA, and Smith-Waterman. As used herein, a homolog is a protein from the same or a different organism that performs the same biological function as the polypeptide to which it is compared. An orthologous relation between two organisms is not necessarily manifest as a one-to-one correspondence between two genes, because a gene can be duplicated or deleted after organism phylogenetic separation, such as speciation. For a given protein, there may be no ortholog or more than one ortholog. Other complicating factors include alternatively spliced transcripts from the same gene, limited gene identification, redundant copies of the same gene with different sequence lengths or corrected sequence. A local sequence alignment program, e.g., BLAST, can be used to search a database of sequences to find similar sequences, and the summary Expectation value (E-value) used to measure the sequence base similarity. As a protein hit with the best E-value for a particular organism may not necessarily be an ortholog or the only ortholog, a reciprocal BLAST search is used in the present invention to filter hit sequences with significant E-values for ortholog identification. The reciprocal BLAST entails search of the significant hits against a database of amino acid sequences from the base organism that are similar to the sequence of the query protein. A hit is a likely ortholog, when the reciprocal BLAST's best hit is the query protein itself or a protein encoded by a duplicated gene after speciation. Thus, homolog is used herein to describe protein that are assumed to have functional similarity by inference from sequence base similarity. The relationship of homologs with amino acid sequences of SEQ ID NO: 479 through SEQ ID NO: 12463 to the proteins with amino acid sequences of SEQ ID NO: 240 through SEQ ID NO: 478 is found is found in Table 2 appended.

A further aspect of the invention comprises functional homolog proteins which differ in one or more amino acids from those of a trait-improving protein disclosed herein as the result of one or more of the well-known conservative amino acid substitutions, e.g., valine is a conservative substitute for alanine and threonine is a conservative substitute for serine. Conservative substitutions for an amino acid within the native sequence can be selected from other members of a class to which the naturally occurring amino acid belongs. Representative amino acids within these various classes include, but are not limited to: (1) acidic (negatively charged) amino acids such as aspartic acid and glutamic acid; (2) basic (positively charged) amino acids such as arginine, histidine, and lysine; (3) neutral polar amino acids such as glycine, serine, threonine, cysteine, tyrosine, asparagine, and glutamine; and (4) neutral nonpolar (hydrophobic) amino acids such as alanine, leucine, isoleucine, valine, proline, phenylalanine, tryptophan, and methionine. Conserved substitutes for an amino acid within a native amino acid sequence can be selected from other members of the group to which the naturally occurring amino acid belongs. For example, a group of amino acids having aliphatic side chains is glycine, alanine, valine, leucine, and isoleucine; a group of amino acids having aliphatic-hydroxyl side chains is serine and threonine; a group of amino acids having amide-containing side chains is asparagine and glutamine; a group of amino acids having aromatic side chains is phenylalanine, tyrosine, and tryptophan; a group of amino acids having basic side chains is lysine, arginine, and histidine; and a group of amino acids having sulfur-containing side chains is cysteine and methionine. Naturally conservative amino acids substitution groups are: valine-leucine, valine-isoleucine, phenylalanine-tyrosine, lysine-arginine, alanine-valine, aspartic acid-glutamic acid, and asparagine-glutamine. A further aspect of the invention comprises proteins that differ in one or more amino acids from those of a described protein sequence as the result of deletion or insertion of one or more amino acids in a native sequence.

Homologs of the trait-improving proteins disclosed provided herein will generally demonstrate significant sequence identity. Of particular interest are proteins having at least 50% sequence identity, more preferably at least about 70% sequence identity or higher, e.g., at least about 80% sequence identity with an amino acid sequence of SEQ ID NO: 240 through SEQ ID NO: 390 and SEQ ID NO: 392 through SEQ ID NO: 478. Of course useful proteins also include those with higher identity, e.g., 90% to 99% identity. Identity of protein homologs is determined by optimally aligning the amino acid sequence of a putative protein homolog with a defined amino acid sequence and by calculating the percentage of identical and conservatively substituted amino acids over the window of comparison. The window of comparison for determining identity can be the entire amino acid sequence disclosed herein, e.g., the full sequence of any of SEQ ID NO: 479 through SEQ ID NO: 12463.

Genes that are homologous to each other can be grouped into families and included in multiple sequence alignments. Then a consensus sequence for each group can be derived. This analysis enables the derivation of conserved and class-(family) specific residues or motifs that are functionally important. These conserved residues and motifs can be further validated with 3D protein structure if available. The consensus sequence can be used to define the full scope of the invention, e.g., to identify proteins with a homolog relationship. Thus, the present invention contemplates that protein homologs include proteins with an amino acid sequence that has at least 90% identity to such a consensus amino acid sequence sequences.

Promoters

Numerous promoters that are active in plant cells have been described in the literature. These include promoters present in plant genomes as well as promoters from other sources, including nopaline synthase (NOS) promoter and octopine synthase (OCS) promoters carried on tumor-inducing plasmids of Agrobacterium tumefaciens, caulimovirus promoters such as the cauliflower mosaic virus or figwort mosaic virus promoters. For instance, see U.S. Pat. Nos. 5,858,742 and 5,322,938 which disclose versions of the constitutive promoter derived from cauliflower mosaic virus (CaMV35S), U.S. Pat. No. 5,378,619 which discloses a Figwort Mosaic Virus (FMV) 35S promoter, U.S. Pat. No. 6,437,217 which discloses a maize RS81 promoter, U.S. Pat. No. 5,641,876 which discloses a rice actin promoter, U.S. Pat. No. 6,426,446 which discloses a maize RS324 promoter, U.S. Pat. No. 6,429,362 which discloses a maize PR-1 promoter, U.S. Pat. No. 6,232,526 which discloses a maize A3 promoter, U.S. Pat. No. 6,177,611 which discloses constitutive maize promoters, U.S. Pat. No. 6,433,252 which discloses a maize L3 oleosin promoter, U.S. Pat. No. 6,429,357 which discloses a rice actin 2 promoter and intron, U.S. Pat. No. 5,837,848 which discloses a root specific promoter, U.S. Pat. No. 6,084,089 which discloses cold inducible promoters, U.S. Pat. No. 6,294,714 which discloses light inducible promoters, U.S. Pat. No. 6,140,078 which discloses salt inducible promoters, U.S. Pat. No. 6,252,138 which discloses pathogen inducible promoters, U.S. Pat. No. 6,175,060 which discloses phosphorus deficiency inducible promoters, U.S. Patent Application Publication 2002/0192813A1 which discloses 5′, 3′ and intron elements useful in the design of effective plant expression vectors, U.S. patent application Ser. No. 09/078,972 which discloses a coixin promoter, U.S. patent application Ser. No. 09/757,089 which discloses a maize chloroplast aldolase promoter, and U.S. patent application Ser. No. 10/739,565 which discloses water-deficit inducible promoters, all of which are incorporated herein by reference. These and numerous other promoters that function in plant cells are known to those skilled in the art and available for use in recombinant polynucleotides of the present invention to provide for expression of desired genes in transgenic plant cells.

Furthermore, the promoters may be altered to contain multiple “enhancer sequences” to assist in elevating gene expression. Such enhancers are known in the art. By including an enhancer sequence with such constructs, the expression of the selected protein may be enhanced. These enhancers often are found 5′ to the start of transcription in a promoter that functions in eukaryotic cells, but can often be inserted in the forward or reverse orientation 5′ or 3′ to the coding sequence. In some instances, these 5′ enhancing elements are introns. Deemed to be particularly useful as enhancers are the 5′ introns of the rice actin 1 and rice actin 2 genes. Examples of other enhancers that can be used in accordance with the invention include elements from the CaMV 35S promoter, octopine synthase genes, the maize alcohol dehydrogenase gene, the maize shrunken 1 gene and promoters from non-plant eukaryotes.

In some aspects of the invention it is preferred that the promoter element in the DNA construct be capable of causing sufficient expression to result in the production of an effective amount of a polypeptide in water deficit conditions. Such promoters can be identified and isolated from the regulatory region of plant genes that are over expressed in water deficit conditions. Specific water-deficit-inducible promoters for use in this invention are derived from the 5′ regulatory region of genes identified as a heat shock protein 17.5 gene (HSP17.5), an HVA22 gene (HVA22), a Rab17 gene and a cinnamic acid 4-hydroxylase (CA4H) gene (CA4H) of Zea maize. Such water-deficit-inducible promoters are disclosed in U.S. application Ser. No. 10/739,565, incorporated herein by reference.

In other aspects of the invention, sufficient expression in plant seed tissues is desired to effect improvements in seed composition. Exemplary promoters for use for seed composition modification include promoters from seed genes such as napin (U.S. Pat. No. 5,420,034), maize L3 oleosin (U.S. Pat. No. 6,433,252), zein Z27 (Russell et al., (1997) Transgenic Res. 6(2):157-166), globulin 1 (Belanger et al., (1991) Genetics 129:863-872), glutelin 1 (Russell (1997) supra), and peroxiredoxin antioxidant (Per1) (Stacy et al., (1996) Plant Mol Biol. 31(6):1205-1216).

In still other aspects of the invention, preferential expression in plant green tissues is desired. Promoters of interest for such uses include those from genes such as SSU (Fischhoff et al., (1992) Plant Mol. Biol. 20:81-93), aldolase and pyruvate orthophosphate dikinase (PPDK) (Taniguchi et al., (2000) Plant Cell Physiol. 41(1):42-48).

Gene Overexpression

“Gene overexpression” used herein in reference to a polynucleotide or polypeptide indicates that the expression level of a target protein, in a transgenic plant or in a host cell of the transgenic plant, exceeds levels of expression in a non-transgenic plant. In a preferred embodiment of the present invention, a recombinant DNA construct comprises the polynucleotide of interest in the sense orientation relative to the promoter to achieve gene overexpression, which is identified as such in Table 1.

Gene Suppression

Gene suppression includes any of the well-known methods for suppressing transcription of a gene or the accumulation of the mRNA corresponding to that gene thereby preventing translation of the transcript into protein. Posttranscriptional gene suppression is mediated by transcription of integrated recombinant DNA to form double-stranded RNA (dsRNA) having homology to a gene targeted for suppression. This formation of dsRNA most commonly results from transcription of an integrated inverted repeat of the target gene, and is a common feature of gene suppression methods known as anti-sense suppression, co-suppression and RNA interference (RNAi). Transcriptional suppression can be mediated by a transcribed dsRNA having homology to a promoter DNA sequence to effect what is called promoter trans suppression.

More particularly, posttranscriptional gene suppression by inserting a recombinant DNA construct with anti-sense oriented DNA to regulate gene expression in plant cells is disclosed in U.S. Pat. No. 5,107,065 (Shewmaker et al.) and U.S. Pat. No. 5,759,829 (Shewmaker et al.). Transgenic plants transformed using such anti-sense oriented DNA constructs for gene suppression can comprise integrated DNA arranged as an inverted repeats that result from insertion of the DNA construct into plants by Agrobacterium-mediated transformation, as disclosed by Redenbaugh et al., in “Safety Assessment of Genetically Engineered Flavr Savr™ Tomato, CRC Press, Inc. (1992). Inverted repeat insertions can comprise a part or all of the T-DNA construct, e.g., an inverted repeat of a complete transcription unit or an inverted repeat of transcription terminator sequence. Screening for inserted DNA comprising inverted repeat elements can improve the efficiency of identifying transformation events effective for gene silencing whether the transformation construct is a simple anti-sense DNA construct which must be inserted in multiple copies or a complex inverted repeat DNA construct (e.g., an RNAi construct) which can be inserted as a single copy.

Posttranscriptional gene suppression by inserting a recombinant DNA construct with sense-oriented DNA to regulate gene expression in plants is disclosed in U.S. Pat. No. 5,283,184 (Jorgensen et al.,) and U.S. Pat. No. 5,231,020 (Jorgensen et al.,). Inserted T-DNA providing gene suppression in plants transformed with such sense constructs by Agrobacterium is organized predominately in inverted repeat structures, as disclosed by Jorgensen et al., Mol. Gen. Genet., 207:471-477 (1987). See also Stam et al. The Plant Journal, 12(1), 63-82 (1997) who used segregation studies to support Jorgensen's finding that gene silencing is mediated by multimeric transgene T-DNA loci in which the T-DNAs are arranged in inverted repeats. Screening for inserted DNA comprising inverted repeat elements can improve the gene silencing efficiency when transforming with simple sense-orientated DNA constructs. Gene silencing efficiency can also be improved by screening for single insertion events when transforming with an RNAi construct containing inverted repeat elements

As disclosed by Redenbaugh et al., gene suppression can be achieved by inserting into a plant genome recombinant DNA that transcribes dsRNA. Such a DNA insert can be transcribed to an RNA element having the 3′ region as a double stranded RNA. RNAi constructs are also disclosed in EP 0426195 A1 (Goldbach et al., 1991) where recombinant DNA constructs for transcription into hairpin dsRNA for providing transgenic plants with resistance to tobacco spotted wilt virus. Double-stranded RNAs were also disclosed in WO 94/01550 (Agrawal et al.,) where anti-sense RNA was stabilized with a self-complementary 3′ segment. Agrawal et al., referred to U.S. Pat. No. 5,107,065 for using such self-stablized anti-sense RNAs for regulating gene expression in plant cells; see International Publication No. 94/01550. Other double-stranded hairpin-forming elements in transcribed RNA are disclosed in International Publication No. 98/05770 (Werner et al.,) where the anti-sense RNA is stabilized by hairpin forming repeats of poly(CG) nucleotides. See also U.S. Patent Application Publication No. 2003/0175965 A1 (Lowe et al.,) which discloses gene suppression using and RNAi construct comprising a gene coding sequence preceded by inverted repeats of 5′UTR. See also U.S. Patent Application Publication No. 2002/0048814 A1 (Oeller) where RNAi constructs are transcribed to sense or anti-sense RNA which is stabilized by a poly(T)-poly(A) tail. See also U.S. Patent Application Publication No. 2003/0018993 A1 (Gutterson et al.,) where sense or anti-sense RNA is stabilized by an inverted repeat of a of the 3′ untranslated region of the NOS gene. See also U.S. Patent Application Publication No. 2003/0036197 A1 (Glassman et al.,) where RNA having homology to a target is stabilized by two complementary RNA regions.

Gene silencing can also be effected by transcribing RNA from both a sense and an anti-sense oriented DNA, e.g., as disclosed by Shewmaker et al., in U.S. Pat. No. 5,107,065 where in Example 1a binary vector was prepared with both sense and anti-sense aroA genes. See also U.S. Pat. No. 6,326,193 where gene targeted DNA is operably linked to opposing promoters.

Gene silencing can also be affected by transcribing from contiguous sense and anti-sense DNA. In this regard see Sijen et al. The Plant Cell, Vol. 8, 2277-2294 (1996) discloses the use of constructs carrying inverted repeats of a cowpea mosaic virus gene in transgenic plants to mediate virus resistance. Such constructs for posttranscriptional gene suppression in plants by double-stranded RNA are also disclosed in International Publication No. WO 99/53050 (Waterhouse et al.,), International Publication No. WO 99/49029 (Graham et al.), U.S. patent application Ser. No. 10/465,800 (Fillatti), U.S. Pat. No. 6,506,559 (Fire et al.). See also U.S. application Ser. No. 10/393,347 (Shewmaker et al.,) that discloses constructs and methods for simultaneously expressing one or more recombinant genes while simultaneously suppressing one or more native genes in a transgenic plant. See also U.S. Pat. No. 6,448,473 (Mitsky et al.,) that discloses multi-gene suppression vectors for use in plants. All of the above-described patents, applications and international publications disclosing materials and methods for posttranscriptional gene suppression in plants are incorporated herein by reference.

Transcriptional suppression such as promoter trans suppression can be affected by a expressing a DNA construct comprising a promoter operably linked to inverted repeats of promoter DNA for a target gene. Constructs useful for such gene suppression mediated by promoter trans suppression are disclosed by Mette et al. The EMBO Journal, Vol. 18, No. 1, pp. 241-148, 1999 and by Mette et al. The EMBO Journal, Vol. 19, No. 19, pp. 5194-5201-148, 2000, both of which are incorporated herein by reference.

Suppression can also be achieved by insertion mutations created by transposable elements may also prevent gene function. For example, in many dicot plants, transformation with the T-DNA of Agrobacterium may be readily achieved and large numbers of transformants can be rapidly obtained. Also, some species have lines with active transposable elements that can efficiently be used for the generation of large numbers of insertion mutations, while some other species lack such options. Mutant plants produced by Agrobacterium or transposon mutagenesis and having altered expression of a polypeptide of interest can be identified using the polynucleotides of the present invention. For example, a large population of mutated plants may be screened with polynucleotides encoding the polypeptide of interest to detect mutated plants having an insertion in the gene encoding the polypeptide of interest.

Gene Stacking

The present invention also contemplates that the trait-improving recombinant DNA provided herein can be used in combination with other recombinant DNA to create plants with a multiple desired traits. The combinations generated can include multiple copies of any one or more of the recombinant DNA constructs.

These stacked combinations can be created by any method, including but not limited to cross breeding of transgenic plants, or multiple genetic transformation.

Plant Transformation Methods

Numerous methods for transforming plant cells with recombinant DNA are known in the art and may be used in the present invention. Two commonly used methods for plant transformation are Agrobacterium-mediated transformation and microprojectile bombardment. Microprojectile bombardment methods are illustrated in U.S. Pat. No. 5,015,580 (soybean); U.S. Pat. No. 5,550,318 (corn); U.S. Pat. No. 5,538,880 (corn); U.S. Pat. No. 5,914,451 (soybean); U.S. Pat. No. 6,160,208 (corn); U.S. Pat. No. 6,399,861 (corn) and U.S. Pat. No. 6,153,812 (wheat) and Agrobacterium-mediated transformation is described in U.S. Pat. No. 5,159,135 (cotton); U.S. Pat. No. 5,824,877 (soybean); U.S. Pat. No. 5,591,616 (corn); and U.S. Pat. No. 6,384,301 (soybean), all of which are incorporated herein by reference. For Agrobacterium tumefaciens based plant transformation system, additional elements present on transformation constructs will include T-DNA left and right border sequences to facilitate incorporation of the recombinant polynucleotide into the plant genome.

In general it is preferred to introduce heterologous DNA randomly, i.e., at a non-specific location, in the genome of a target plant line. In special cases it may be useful to target heterologous DNA insertion in order to achieve site-specific integration, e.g., to replace an existing gene in the genome, to use an existing promoter in the plant genome, or to insert a recombinant polynucleotide at a predetermined site known to be active for gene expression. Several site specific recombination systems exist which are known to function implants include cre-lox as disclosed in U.S. Pat. No. 4,959,317 and FLP-FRT as disclosed in U.S. Pat. No. 5,527,695, both incorporated herein by reference.

Transformation methods of this invention are preferably practiced in tissue culture on media and in a controlled environment. “Media” refers to the numerous nutrient mixtures that are used to grow cells in vitro, that is, outside of the intact living organism. Recipient cell targets include, but are not limited to, meristem cells, callus, immature embryos and gametic cells such as microspores, pollen, sperm and egg cells. It is contemplated that any cell from which a fertile plant may be regenerated is useful as a recipient cell. Callus may be initiated from tissue sources including, but not limited to, immature embryos, seedling apical meristems, microspores and the like. Cells capable of proliferating as callus are also recipient cells for genetic transformation. Practical transformation methods and materials for making transgenic plants of this invention, e.g., various media and recipient target cells, transformation of immature embryos and subsequent regeneration of fertile transgenic plants are disclosed in U.S. Pat. Nos. 6,194,636 and 6,232,526 and U.S. patent application Ser. No. 09/757,089, which are incorporated herein by reference.

In practice DNA is introduced into only a small percentage of target cells in any one experiment. Marker genes are used to provide an efficient system for identification of those cells that are stably transformed by receiving and integrating a transgenic DNA construct into their genomes. Preferred marker genes provide selective markers that confer resistance to a selective agent, such as an antibiotic or herbicide. Potentially transformed cells are exposed to the selective agent. In the population of surviving cells will be those cells where, generally, the resistance-conferring gene has been integrated and expressed at sufficient levels to permit cell survival. Cells may be tested further to confirm stable integration of the exogenous DNA. Useful selective marker genes include those conferring resistance to antibiotics such as kanamycin (nptII), hygromycin B (aph IV) and gentamycin (aac3 and aacC4) or resistance to herbicides such as glufosinate (bar or pat) and glyphosate (EPSPS). Examples of such selectable are illustrated in U.S. Pat. Nos. 5,550,318; 5,633,435; 5,780,708 and 6,118,047, all of which are incorporated herein by reference. Screenable markers which provide an ability to visually identify transformants can also be employed, e.g., a gene expressing a colored or fluorescent protein such as a luciferase or green fluorescent protein (GFP) or a gene expressing a beta-glucuronidase or uidA gene (GUS) for which various chromogenic substrates are known. It is also contemplated that combinations of screenable and selectable markers will be useful for identification of transformed cells. See PCT publication WO 99/61129 which discloses use of a gene fusion between a selectable marker gene and a screenable marker gene, e.g., an NPTII gene and a GFP gene.

Cells that survive exposure to the selective agent, or cells that have been scored positive in a screening assay, may be cultured in regeneration media and allowed to mature into plants. Developing plantlets can be transferred to soil less plant growth mix, and hardened off, e.g., in an environmentally controlled chamber at about 85% relative humidity, 600 ppm CO₂, and 25-250 microeinsteins m⁻² s⁻¹ of light, prior to transfer to a greenhouse or growth chamber for maturation. Plants are preferably matured either in a growth chamber or greenhouse. Plants are regenerated from about 6 wk to 10 months after a transformant is identified, depending on the initial tissue. During regeneration, cells are grown to plants on solid media at about 19 to 28° C. After regenerating plants have reached the stage of shoot and root development, they may be transferred to a greenhouse for further growth and testing. Plants may be pollinated using conventional plant breeding methods known to those of skill in the art and seed produced.

Progeny may be recovered from transformed plants and tested for expression of the exogenous recombinant polynucleotide. Useful assays include, for example, “molecular biological” assays, such as Southern and Northern blotting and PCR; “biochemical” assays, such as detecting the presence of RNA, e.g., double stranded RNA, or a protein product, e.g., by immunological means (ELISAs and Western blots) or by enzymatic function; plant part assays, such as leaf or root assays; and also, by analyzing the phenotype of the whole regenerated plant.

Discovery of Trait-improving Recombinant DNA

To identify recombinant DNA that confer improved traits to plants, Arabidopsis thaliana was transformed with a candidate recombinant DNA construct and screened for an improved trait.

Arabidopsis thaliana is used a model for genetics and metabolism in plants. Arabidopsis has a small genome, and well documented studies are available. It is easy to grow in large numbers and mutants defining important genetically controlled mechanisms are either available, or can readily be obtained. Various methods to introduce and express isolated homologous genes are available (see Koncz, et al., eds. Methods in Arabidopsis Research. et al., (1992), World Scientific, New Jersey, New Jersey, in “Preface”).

A two-step screening process was employed which comprised two passes of trait characterization to ensure that the trait modification was dependent on expression of the recombinant DNA, but not due to the chromosomal location of the integration of the transgene. Twelve independent transgenic lines for each recombinant DNA construct were established and assayed for the transgene expression levels. Five transgenic lines with high transgene expression levels were used in the first pass screen to evaluate the transgene's function in T2 transgenic plants. Subsequently, three transgenic events, which had been shown to have one or more improved traits, were further evaluated in the second pass screen to confirm the transgene's ability to impart an improved trait. The following Table 3 summarizes the improved traits that have been confirmed as provided by a recombinant DNA construct.

In particular Table3 reports “PEP SEQ ID NO” which is the amino acid sequence of the protein cognate to the DNA in the recombinant DNA construct corresponding to a protein sequence of a SEQ ID NO. in the Sequence Listing; “construct_id” is an arbitrary name for the recombinant DNA describe more particularly in Table 1; “annotation” refers to a description of the top hit protein obtained from an amino acid sequence query of each PEP SEQ ID NO to GenBank database of the National Center for Biotechnology Information (ncbi). More particularly, “gi” is the GenBank ID number for the top BLAST hit; “description” refers to the description of the top BLAST hit; “e-value” provides the expectation value for the BLAST hit; “identity” refers to the percentage of identically matched amino acid residues along the length of the portion of the sequences which is aligned by BLAST between the sequence of interest provided herein and the hit sequence in GenBank; “traits” identifies by two letter code the confirmed improvement in a transgenic plant provided by the recombinant DNA. The codes for improved traits are: “CK” which indicates cold tolerance improvement identified under a cold shock tolerance screen; “CS” which indicates cold tolerance improvement identified by a cold germination tolerance screen; “DS” which indicates drought tolerance improvement identified by a drought stress tolerance screen; “PEG” which indicates osmotic stress tolerance improvement identified by a PEG induced osmotic stress tolerance screen; “HS” which indicates heat stress tolerance improvement identified by a heat stress tolerance screen; “SS” which indicates high salinity stress tolerance improvement identified by a salt stress tolerance screen; “LN” which: indicates nitrogen use efficiency improvement identified by a low nitrogen tolerance screen. “LL” which indicates attenuated shade avoidance response identified by a shade tolerance screen under a low light condition; “PP” which indicates improved growth and development at early stages identified by an early plant growth and development screen; “SP” which indicates improved growth and development at late stages identified by a late plant growth and development screen provided herein.

TABLE 3 PEP SEQ con- Annotation ID NO struct_id e-value identity gi Description traits 240 19867 2.00E−72  47 15226242 (NM_128336) hypothetical protein CK CS [Arabidopsis thaliana] 241 74518 0 100 17980436 bacteriophytochrome DS LN PEG PP CK CS [Pseudomonas fluorescens] 242 15816 1.00E−101 100 18414706 (NM_120565) expressed protein CK [Arabidopsis thaliana] dbj|BAB08987.1 243 17918 5.00E−78  81 15232662 (AB017071) zinc finger protein-like; SS CK Ser/Thr protein kinase-like protein [Arabidopsis thaliana] 244 15306 1.00E−121 57 15227057 (NM_126342) predicted by genefinder CS and genscan [Arabidopsis thaliana] 245 12038 2.00E−47  100 18413298 auxin-regulated protein PP CS [Arabidopsis thaliana] gi|30681325|ref|NP_849354.1 246 12046 CS 247 13432 1.00E−79  53 18396732 (NM_111270) expressed protein CS [Arabidopsis thaliana] gb|AAF05858.1 248 13711 1.00E−33  84 15232724 expressed protein CS [Arabidopsis thaliana] gi|11280688|pir||T45643 hypothetical protein 249 14809 1.00E−142 100 15230177 AF488576_1 (AF488576) putative bHLH CS transcription factor [Arabidopsis thaliana] 250 14951 1.00E−146 100 4056434 (AC005990) Similar to OBP32pep PP CS protein gb|U37698 from Arabidopsis thaliana 251 15632 0 89 9758356 (AB013396) eukaryotic initiation CS factor 4, eIF4-like protein [Arabidopsis thaliana] 252 16147 0 100 11890406 (AF197940) SAM: phosphoethanolamine CS N-methyltransferase [Arabidopsis thaliana] g 253 16158 1.00E−68  100 18412355 (NM_106587) expressed protein CS [Arabidopsis thaliana] 254 16170 2.00E−82  91 15224757 (NM_127488) putative small heat CS shock protein [Arabidopsis thaliana] 255 16171 4.00E−92  72 18401372 (NM_128284) expressed protein CS [Arabidopsis thaliana] 256 16175 1.00E−157 85 15240715 (NM_126137) putative protein CS [Arabidopsis thaliana] 257 17430 1.00E−155 90 13878155 (AF370340) putative mitochondrial CS dicarboxylate carrier protein [Arabidopsis thaliana] 258 17819 1.00E−140 95 15236507 (NM_116915) hypothetical protein SS CS [Arabidopsis thaliana] emb|CAB77971.1 259 17921 1.00E−110 74 18415982 (NM_118393) HSP associated protein CS like [Arabidopsis thaliana] 260 17928 1.00E−74  100 15231105 (NM_115730) transcriptional PP CS coactivator - like protein [Arabidopsis thaliana] 261 18637 1.00E−128 87 15233509 (NM_118226) putative protein CS [Arabidopsis thaliana] 262 18816 0 94 18398254 (NM_102942) expressed protein LL CS [Arabidopsis thaliana] 263 19227 1.00E−164 96 15219482 (NM_106009) MAP kinase, putative CS [Arabidopsis thaliana] 264 19429 0 100 15237038 (NM_118860) GH3 like protein CS [Arabidopsis thaliana] 265 70235 2.00E−94  100 15234243 (NM_117229) phospholipid PP CS hydroperoxide glutathione peroxidase [Arabidopsis thaliana] 266 72634 4.00E−52  86 30699033 GAST1-related protein CS [Arabidopsis thaliana] 267 72752 0 100 6319971 (NC_001136) phosphotyrosine-specific PP CS protein phosphatase; Ptp1p [Saccharomyces cerevisiae] 268 12007 1.00E−119 76 15236117 (NM_118746) uncharacterized protein HS [Arabidopsis thaliana] 269 12290 5.00E−66  92 18396460 (NM_111186) expressed protein HS [Arabidopsis thaliana]] 270 12343 1.00E−111 61 18414724 (NM_120571) expressed protein HS [Arabidopsis thaliana] gb|AAF61902.1|AF208051_1 (AF208051) small heat shock-like protein 271 14348 0 100 15234254 (NM_118912) putative protein HS [Arabidopsis thaliana] pir||T05878 isp4 protein homolog T29A15.220 272 15708 7.00E−71  87 18394214 (NM_101391) expressed protein HS [Arabidopsis thaliana] 273 17615 1.00E−108 85 18414711 (NM_120567) expressed protein CS HS [Arabidopsis thaliana] 274 17622 0 93 15238837 (NM_121852) putative protein HS [Arabidopsis thaliana] 275 70714 0 94 7446439 probable serine/threonine-specific HS protein kinase (EC 2.7.1.—) F1715.140 - Arabidopsis thaliana emb|CAA19877.1| (AL031032) protein kinase-like protein [Arabidopsis thaliana] 276 17925 1.00E−157 82 18405518 (NM_129646) expressed protein HS CK [Arabidopsis thaliana] pir||00747 RING-H2 finger protein RHC1a 277 18541 1.00E−128 83 15237100 (NM_119735) hypothetical protein HS CS [Arabidopsis thaliana] 278 11425 1.00E−155 100 18405364 (AB024028) 20S proteasome beta subunit; HS multicatalytic endopeptidase [Arabidopsis thaliana] 279 12263 9.00E−39  100 15241279 small zinc finger-related protein HS [Arabidopsis thaliana] gi|12230183|sp|Q9XGY4|IM08_ARATH Mitochondrial import inner membrane translocase subunit Tim8 280 12288 0 97 7488126 AAB01678.1| (U27590) Fe(II) transport HS protein [Arabidopsis thaliana] 281 12910 0 90 17065456 (AY062804) A6 anther-specific protein HS [Arabidopsis thaliana] 282 14335 0 93 15229692 (NM_111953) omega-3 fatty acid LL HS desaturase, chloroplast precursor [Arabidopsis thaliana] 283 17427 0 100 13878127 (AF370326) putative 2-nitropropane HS dioxygenase [Arabidopsis thaliana] 284 19140 0 100 15223458 (NM_104489) SAR DNA binding protein, HS putative [Arabidopsis thaliana] gb|AAF02835.1|AC009894_6 (AC009894) nucleolar protein [Arabidopsis thaliana] gb|AAG40838.1|AF302492_1 (AF302492) NOP56-like protein [Arabidopsis thaliana] 285 19179 7.00E−97  92 18390408 (NM_100335) expressed protein PP SS HS [Arabidopsis thaliana] gb|AAB80630.1| (AC002376) Strong similarity to Triticum ABA induced membrane protein (gb|U80037) 286 19251 0 100 21553584 (AY085451) putative 3-isopropylmalate HS dehydrogenase [Arabidopsis thaliana] 287 19443 1.00E−171 100 15220490 (NM_102700) zinc finger protein, HS putative [Arabidopsis thaliana] gb|AAG51745.1|AC068667_24 (AC068667) zinc finger protein, putative; 86473-88078 [Arabidopsis thaliana] 288 19607 0 90 15239867 (NM_124313) xylosidase HS [Arabidopsis thaliana] 289 19915 2.00E−87  50 15229221 (NM_111278) NAM-like protein (no SP HS apical meristem) [Arabidopsis thaliana] 290 70222 0 97 15240523 (NM_124341) amino acid permease 6 DS PP HS (emb|CAA65051.1) [Arabidopsis thaliana] 291 70464 1.00E−106 92 15233481 (NM_118221) putative protein HS [Arabidopsis thaliana] 292 70474 1.00E−148 99 20127049 (AF488587) putative bHLH transcription HS factor [Arabidopsis thaliana] 293 70484 0 93 18418491 (NM_119632) putative protein CS PP HS [Arabidopsis thaliana] 294 72474 1.00E−129 81 14150732 (AF374475) hypersensitive-induced PP HS response protein [Oryza sativa] 295 13047 1.00E−170 86 15237573 (NM_123481) purine permease-like LL protein [Arabidopsis thaliana] dbj|BAB09718.1| (AB010072) purine permease-like protein [Arabidopsis thaliana] 296 13304 0 92 15227905 (NM_127337) putative LL senescence-associated protein 12 [Arabidopsis thaliana] 297 13474 0 97 2318131 (AF014824) histone deacetylase LL [Arabidopsis thaliana] 298 19252 3.00E−85  100 18397475 (NM_111486) putative dual-specificity PP LL SS HS CS protein phosphatase [Arabidopsis thaliana] 299 12612 7.00E−84  67 18397426 (NM_111472) expressed protein LL [Arabidopsis thaliana] 300 12926 2.00E−08  63 18407064 expressed protein LL [Arabidopsis thaliana] gi|25408990|pir|| 301 13230 3.00E−68  83 15233017 (NM_111160) unknown protein LL [Arabidopsis thaliana] 302 14235 1.00E−142 82 18402650 (NM_103835) expressed protein LL [Arabidopsis thaliana] 303 17305 0 100 15222179 (NM_100550) sugar kinase, putative LL [Arabidopsis thaliana] 304 17470 1.00E−138 76 15219110 AAD17313.1 |(AF 123310) NAC domain LL protein NAM [Arabidopsis thaliana] 305 17718 2.00E−91  91 15228362 (NM_114694) putative protein LL [Arabidopsis thaliana] 306 17904 0 97 18399578 (NM_112070) expressed protein LL [Arabidopsis thaliana] 307 18280 0 97 18398767 AAM66940.1| (AY088617) DS LL membrane-associated salt-inducible protein like [Arabidopsis thaliana] 308 18287 1.00E−148 100 15223439 (NM_100045) polyphosphoinositide LL binding protein, putative [Arabidopsis thaliana] 309 18501 0 94 18418838 (NM_121863) putative protein LL [Arabidopsis thaliana] gb|AAG35778.1|AF280057_1 (AF280057) tonneau 2 [Arabidopsis thaliana] 310 18877 1.00E−85  100 18408502 (NM_105311) calmodulin-related protein LL [Arabidopsis thaliana] 311 19531 0 98 15241970 (NM_125674) 1-deoxy-D-xylulose LL 5-phosphate reductoisomerase (DXR) [Arabidopsis thaliana] 312 70405 0 85 18390592 (NM_100475) expressed protein SS LL [Arabidopsis thaliana] 313 72136 2.00E−37  66 123379 HMG1/2-like protein (SB11 protein) LL gi|99914|pir||S22309 high mobility group protein HMG-1 - soybean gi|18645|emb|CAA41200.1| HMG-1 like protein gene [Glycine max] 314 72611 1.00E−102 82 6721504 (AP001072) hypothetical protein LL [Oryza sativa (japonica cultivar-group)] 315 12627 0 100 15236663 (NM_118524) UDPglucose LN 4-epimerase - like protein [Arabidopsis thaliana] 316 12813 0 96 2454184 (U80186) pyruvate dehydrogenase E1 LN beta subunit [Arabidopsis thaliana] 317 14945 1.00E−122 92 18400517 (NM_112338) expressed protein LN [Arabidopsis thaliana] dbj|BAB02642.1| (AP002061) MtN3-like protein 318 15345 0 97 15237392 (NM_123987) ornithine LN aminotransferase [Arabidopsis thaliana] 319 15348 0 81 18414239 (NM_117530) expressed protein LN [Arabidopsis thaliana] 320 16325 1.00E−105 100 15225174 (NM_128763) putative alanine acetyl LN transferase [Arabidopsis thaliana] gb|AAD15401.1 321 16702 0 77 18408943 (NM_105480) expressed protein LN [Arabidopsis thaliana] sp|Q9M647|IAR1_ARATH IAA-alanine resistance protein 1 322 16836 0 100 11692854 AF327534_1 (AF327534) putative LN adenosine triphosphatase [Arabidopsis thaliana] 323 17002 1.00E−138 56 18414140 (NM_117486) Expressed protein LN [Arabidopsis thaliana] gb|AAK68800.1| (AY042860) Unknown protein [Arabidopsis thaliana] 324 17012 3.00E−79  100 18398187 (NM_127222) actin depolymerizing LN factor 5 [Arabidopsis thaliana] 325 17017 1.00E−155 86 11358585 nuclear envelope membrane protein-like - LN Arabidopsis thaliana 326 17344 3.00E−49  100 18424201 SKP1 family [Arabidopsis thaliana] PP LN gi|9759236|dbj|BAB09760.1| contains similarity to elongin C~gene_id: MNC17.5 [Arabidopsis thaliana] gi|15028385|gb|AAK76669.1| putative elongin protein] 327 17426 0 95 15238801 (NM_124151) farnesyl diphosphate LN synthase precursor (gb|AAB49290.1) [Arabidopsis thaliana] 328 17655 1.00E−129 86 15227472 (NM_129758) putative C2H2-type zinc LN finger protein [Arabidopsis thaliana] 329 17656 1.00E−135 74 15233081 (NM_115995) putative DNA-binding LN protein [Arabidopsis thaliana] 330 17906 1.00E−129 100 18378887 (NM_100065) expressed protein PP LN [Arabidopsis thaliana] 331 18278 0 95 15220147 (NM_103617) Cyclin, putative LN [Arabidopsis thaliana] 332 18822 0 92 15232759 (NM_111813) putative protein kinase LN [Arabidopsis thaliana] 333 18881 0 100 18401029 (NM_112485) putative L-asparaginase LN [Arabidopsis thaliana] 334 19213 2.00E−70  91 18408726 (NM_105394) expressed protein LN [Arabidopsis thaliana] 335 19239 1.00E−59  100 15235876 DNA-directed RNA polymerase LN subunit -related [Arabidopsis thaliana] gi|25313101|pir||A85078 336 19247 1.00E−81  53 9711883 (AP002524) hypothetical protein~similar LN to Drosophila melanogaster chromosome 3L, CG10171 gene product [Oryza sativa (japonica cultivar-group)] 337 19460 1.00E−146 80 15238816 (NM_121850) AP2-domain DNA-binding LN protein-like [Arabidopsis thaliana] 338 19512 0 85 15237502 (NM_124046) bHLH protein-like LN [Arabidopsis thaliana] 339 19533 0 99 18395911 (NM_102409) expressed protein LN [Arabidopsis thaliana] 340 19603 0 87 18403383 (NM_113143) expressed protein LN [Arabidopsis thaliana] dbj|BAB01784.1| (AB022215) hydroxyproline-rich glycoprotein [Arabidopsis thaliana] 341 72126 5.00E−78  53 12005328 (AF239956) unknown LN [Hevea brasiliensis] 342 72437 8.00E−89  92 11994756 (AP001313) kinetechore (Skp1p-like) LN protein-like [Arabidopsis thaliana] 343 72441 5.00E−95  84 15218602 (NM_100157) ribosomal protein L19, LN putative [Arabidopsis thaliana] 344 72639 2.00E−73  91 18403896 (NM_104101) expressed protein LN [Arabidopsis thaliana] 345 14825 0 93 15242814 (NM_120445) protein kinase-like PEG protein [Arabidopsis thaliana] 346 17931 1.00E−136 68 15242003 (NM_125688) Dof zinc finger PEG CS protein - like [Arabidopsis thaliana] 347 18854 1.00E−164 79 18423918 (NM_125077) nucleosome assembly PEG HS protein [Arabidopsis thaliana] 348 12237 1.00E−21  76 18398176 expressed protein PEG [Arabidopsis thaliana] gi|12322743|gb|AAG51367.1|AC012562_28 349 13414 2.00E−69  92 12324443 (AC012329) unknown protein; PEG 50647-51606 [Arabidopsis thaliana] 350 16160 1.00E−176 87 18415888 (NM_118352) putative protein PEG [Arabidopsis thaliana] 351 16226 1.00E−138 96 9294682 (AP001305) contains similarity to HS PEG RNA polymerase transcriptional regulation mediator~gene_id: MHC9.3 [Arabidopsis thaliana] 352 16803 1.00E−146 90 18394201 (NM_101382) expressed protein PEG [Arabidopsis thaliana] gb|AAD39643.1|AC007591_8 (AC007591) Contains a PF|00175 Oxidoreductase FAD/NADH-binding domain. 353 18260 0 100 15219795 (NM_100349) putative K+ channel, PEG beta subunit [Arabidopsis thaliana] 354 18642 2.00E−68  71 15235819 (NM_118411) predicted protein PP PEG [Arabidopsis thaliana] 355 18721 3.00E−21  53 18408611 glycine-rich protein PEG [Arabidopsis thaliana] gi|12597766|gb|AAG60079.1|AC013288_13 356 19254 0 96 18398480 (NM_111769) expressed protein PEG [Arabidopsis thaliana] 357 70247 0 95 15238559 (NM_122954) glutamate-ammonia ligase CS DS HS PP PEG (EC 6.3.1.2) precursor, chloroplast (clone lambdaAtgsl1) (pir||S18600) [Arabidopsis thaliana] 358 70650 1.00E−83  57 18399283 (NM_127582) expressed protein PP PEG [Arabidopsis thaliana] 359 12635 0 97 15231953 (NM_111700) putative non-phototropic HS hypocotyl [Arabidopsis thaliana] 359 11787 0 97 15231953 (NM_111700) putative non-phototropic PP hypocotyl [Arabidopsis thaliana] 360 13641 1.00E−42  87 15218189 dynein light chain -related PP [Arabidopsis thaliana] gi|25405535|pir||E96562 361 14515 0 71 15128395 (AP003255) contains ESTs PP AU100655(C11462), C26007 (C11462)~similar to Arabidopsis thaliana chromosome 3, F24B22.150-unknown protein [Oryza sativa (japonica cultivar-group)] 362 14920 0 100 4239819 (AB010875) PHR1 [Arabidopsis thaliana] PP 363 15204 0 96 15230379 (NM_112829) putative tyrosine PP phosphatase [Arabidopsis thaliana] 364 19058 0 96 18396298 (NM_102496) expressed protein LN [Arabidopsis thaliana] 364 15216 0 96 18396298 (NM_102496) expressed protein PP [Arabidopsis thaliana] 365 15330 5.00E−68  59 18400296 (NM_112272) expressed protein PP [Arabidopsis thaliana] 366 19610 0 100 18409509 (NM_115079) expressed protein PP CS [Arabidopsis thaliana] 367 14338 0 100 15222967 (NM_103926) sterol delta7 reductase PP HS CS [Arabidopsis thaliana] sp 368 17809 0 100 15242240 (NM_124576) sorbitol dehydrogenase-like PP HS protein [Arabidopsis thaliana] 369 72471 3.00E−83  52 18395821 (NM_111011) expressed protein DS PP HS [Arabidopsis thaliana] 370 16403 1.00E−176 73 15237042 (NM_117178) 98b like protein PP LL LN [Arabidopsis thaliana] p 371 17737 0 86 15240924 (NM_122624) RING-H2 zinc finger PP LN protein-like [Arabidopsis thaliana] 372 18395 0 84 18401775 (NM_128415) putative AP2 domain SS PP LN transcription factor [Arabidopsis thaliana] 373 72772 0 100 15226228 (NM_128328) putative cytochrome P450 HS SP PP LN [Arabidopsis thaliana] 374 19441 0 85 9294477 (AB018114) RING finger protein-like PP PEG [Arabidopsis thaliana] 375 10486 1.00E−99  100 15237535 (NM_120465) Terminal flower1 (TFL1) PP [Arabidopsis thaliana] 376 11409 1.00E−133 100 68888 trichome differentiation protein GL1 - CS LN SS PP Arabidopsis thaliana 377 12104 1.00E−132 92 15230178 AF488577_1 (AF488577) putative bHLH PP transcription factor [Arabidopsis thaliana] 378 12258 1.00E−22  59 21554390 arabinogalactan-protein PP [Arabidopsis thaliana] 379 12909 0 100 18398696 (NM_111831) expressed protein PP [Arabidopsis thaliana] 380 14310 0 96 15226784 (NM_129655) unknown protein PP [Arabidopsis thaliana] 381 14317 0 100 18395560 (NM_126399) expressed protein PP [Arabidopsis thaliana] 382 14709 0 91 15219676 (NM_100303) putative beta-ketoacyl-CoA PP synthase [Arabidopsis thaliana] pir||T00951 probable 3-oxoacyl-[acyl-carrier-protein] synthase (EC 2.3.1.41) F20D22.1 383 15123 0 97 15238451 (NM_120596) putative protein PP [Arabidopsis thaliana] 384 16013 4.00E−91  85 15241799 (NM_125629) ripening-related PP protein-like [Arabidopsis thaliana] 385 16185 0 95 18420375 (NM_120069) cysteine proteinase PP RD19A [Arabidopsis thaliana] 386 16719 0 100 18401703 (NM_103632) expressed protein PP [Arabidopsis thaliana] 387 17490 8.00E−93  92 18405248 (NM_104392) expressed protein PP [Arabidopsis thaliana] 388 17905 8.00E−75  69 18404002 (NM_113306) PHD-finger protein, PP putative [Arabidopsis thaliana] 389 18385 1.00E−117 100 15223626 (NM_104559) integral membrane PP protein, putative [Arabidopsis thaliana] 390 18392 0 95 15227193 (NM_127194) putative homeodomain SS PP transcription factor [Arabidopsis thaliana] 392 18531 1.00E−142 100 15242792 (NM_125746) putative protein PP [Arabidopsis thaliana] 393 18603 0 94 18415840 (NM_118332) alcohol dehydrogenase PP like protein [Arabidopsis thaliana] 394 19530 0 96 15242217 (NM_122138) Ruv DNA-helicase-like PP protein [Arabidopsis thaliana] 395 70202 0 61 15241293 (NM_121408) putative protein HS PP [Arabidopsis thaliana] 396 72009 0 91 6319543 (NC_001134) Amino acid transport PP protein for valine, leucine, isoleucine, and tyrosine; Tat1p [Saccharomyces cerevisiae] 397 72119 3.00E−70  57 126078 LATE EMBRYOGENESIS ABUNDANT PP PROTEIN D-34 (LEA D-34) 398 10188 0 92 15228011 (NM_129846) putative cytochrome P450 DS [Arabidopsis thaliana] 399 10404 1.00E−151 94 99713 homeotic protein agamous - DS Arabidopsis thaliana 400 11333 1.00E−145 100 7207994 (AF083220) proliferating cellular DS nuclear antigen [Arabidopsis thaliana] 401 11719 0 87 15240257 (NM_126126) cyclin D3-like protein DS [Arabidopsis thaliana] 402 13663 1.00E−152 94 15227497 (NM_129769) unknown protein DS [Arabidopsis thaliana] 403 13958 0 96 15222885 (NM_101226) SP DS aminoalcoholphosphotransferase [Arabidopsis thaliana] 404 15214 0 92 15223772 (NM_106341) Tub family protein, DS putative [Arabidopsis thaliana] 405 10483 2.00E−86  100 15223944 (NM_100757) superoxidase dismutase SP DS [Arabidopsis thaliana] 406 11711 0 100 15234217 (NM_19505) 2-dehydro-3-deoxyphospho- DS heptonate aldolase [Arabidopsis thaliana] 407 11909 1.00E−126 88 99735 L-ascorbate peroxidase (EC 1.11.1.11) DS precursor - Arabidopsis thaliana (fragment) 408 12216 0 100 15236949 (NM_118837) putative protein DS [Arabidopsis thaliana] 409 12236 2.00E−55  100 15231278 pollen specific protein -related DS [Arabidopsis thaliana] 410 12256 0 100 2317731 (AF013628) reversibly glycosylated DS polypeptide-2 [Arabidopsis thaliana] 411 12806 1.00E−157 86 15235640 (NM_119926) putative protein DS [Arabidopsis thaliana] 412 12904 0 96 15239631 BAA97512.1| (AB026634) 3′(2′), SP DS 5′-bisphosphate nucleotidase protein-like protein [Arabidopsis thaliana] 413 13212 4.00E−74  93 15236917 (AL161566) putative protein DS [Arabidopsis thaliana] 414 13232 5.00E−30  60 15223263 expressed protein DS [Arabidopsis thaliana] gi|7485996|pir||T00711 415 13912 9.00E−68  100 18406846 O64644|SP18_ARATH Probable Sin3 DS associated polypeptide [Arabidopsis thaliana] 416 14327 0 92 15221444 (NM_102795) putative GTP-binding DS protein [Arabidopsis thaliana] 417 14704 3.00E−71  46 17228240 (NC_003272) hypothetical protein DS [Nostoc sp. PCC 7120] 418 14714 0 94 15219541 (NM_106032) ethylene-insensitive3-like3 DS (EIL3) [Arabidopsis thaliana] 419 15142 0 74 15235217 (NM_118107) putative protein SP DS [Arabidopsis thaliana] 420 17450 1.00E−169 100 15232066 AAF26152.1|AC008261_9 (AC008261) DS putative homeobox-leucine zipper protein, HAT7 [Arabidopsis thaliana] 421 18607 1.00E−151 94 15221373 (NM_105503) putative transcription DS factor [Arabidopsis thaliana] 422 19409 0 73 15241667 (NM_120281) putative homeodomain DS protein [Arabidopsis thaliana] 423 19412 0 96 15228826 (NM_116132) putative protein DS [Arabidopsis thaliana] 424 13005 0 99 15239405 (NM_122447) cyclin 3a SP SS PEG [Arabidopsis thaliana] gb|AAC98445.1| (AC006258) cyclin 3a [Arabidopsis thaliana] 425 10203 0 81 18405485 (NM_104444) expressed protein SP [Arabidopsis thaliana] 426 11327 0 92 12643807 Protein farnesyltransferase alpha SP subunit (CAAX farnesyltransferase alpha subunit) (RAS proteins prenyltransferase alpha) (FTase-alpha)[Arabidopsis thaliana] 427 12018 1.00E−175 96 18404664 (NM_129374) expressed protein LL [Arabidopsis thaliana] 427 11814 1.00E−175 96 18404664 (NM_129374) expressed protein SP [Arabidopsis thaliana] 428 13003 1.00E−169 85 18394319 (NM_101474) expressed protein SP [Arabidopsis thaliana] 429 13949 1.00E−160 85 18399097 (NM_103124) expressed protein SP [Arabidopsis thaliana] 430 16416 1.00E−161 94 15236283 (NM_116570) putative chloroplast SP protein import component [Arabidopsis thaliana] 431 16438 1.00E−167 78 18403775 (AC004667) expressed protein SP [Arabidopsis thaliana] gb|AAM62820.1| (AY085599) zinc finger protein Glo3-like [Arabidopsis thaliana] 432 17124 0 100 15221491 (NM_104934) similar to flavin- SP containing monooxygenase (sp|P36366); similar to ESTs gb|R30018, gb|H36886, gb|N37822, and gb|T88100 [Arabidopsis thaliana] 433 19132 0 92 18396094 (NM_111084) expressed protein SP [Arabidopsis thaliana] 434 17922 1.00E−134 83 7485939 AAC13593.1| (AF058914) contains LL SP CS similarity to Arabidopsis thaliana DNA-damage-repair/tolerance resistance protein DRT111 (SW: P42698) 435 19719 1.00E−141 72 6692816 (AB036735) allyl alcohol dehydrogenase PEG SP HS [Nicotiana tabacum] 436 14274 8.00E−90  100 18407428 (NM_130339) expressed protein SP [Arabidopsis thaliana] 436 17336 8.00E−90  100 18407428 (NM_130339) expressed protein SP LL [Arabidopsis thaliana] 437 17735 1.00E−108 91 18404601 (NM_129353) expressed protein SP LL [Arabidopsis thaliana] 438 19249 5.00E−43  100 21553354 glycine-rich RNA binding protein 7 PP SP LN [Arabidopsis thaliana] 439 18513 0 96 15226492 (NM_130274) putative protein kinase SP PP SS [Arabidopsis thaliana] pir||T02181 protein kinase homolog F14M4.11 440 11517 1.00E−153 85 18412044 (NM_106509) expressed protein SP [Arabidopsis thaliana] 441 12363 0 100 15242458 (NM_123934) GDSL-motif lipase/ SP hydrolase-like protein [Arabidopsis thaliana] 442 12922 7.00E−81  100 18403216 (NM_128881) expressed protein SP [Arabidopsis thaliana] 443 15360 1.00E−152 89 18398108 (NM_111674) expressed protein SP [Arabidopsis thaliana] 444 16028 0 100 15232435 (NM_115274) peptide transport-like SP protein [Arabidopsis thaliana] 445 16648 1.00E−134 100 15891409 NP_534027.1| (NC_003305) SP 3-oxoacyl-(acyl-carrier-protein) reductase [Agrobacterium tumefaciens str. C58 (U. Washington)] 446 16705 0 95 15236458 (NM_116899) nodulin-like protein SP [Arabidopsis thaliana] 447 16715 0 96 15238198 (NM_120537) putative protein SP [Arabidopsis thaliana] 448 17316 1.00E−124 95 18378907 (NM_100079) expressed protein SP [Arabidopsis thaliana] 449 17331 0 85 15220100 (NM_106680) putative sulfate SP transporter [Arabidopsis thaliana] 450 17339 2.00E−79  100 15228208 (NM_114633) putative protein SP [Arabidopsis thaliana] 451 17420 1.00E−124 94 15229782 (NM_114248) glutathione SP transferase-like protein [Arabidopsis thaliana] 452 17446 1.00E−144 88 15230344 (NM_115620) AP2 transcription SP factor - like protein [Arabidopsis thaliana] 453 17487 1.00E−71  78 15218649 (NM_102603) ethylene-responsive SP element binding factor, putative [Arabidopsis thaliana] 454 17740 0 97 15232593 (NM_114527) scarecrow-like protein SP [Arabidopsis thaliana] 455 17752 1.00E−176 94 9755372 (AC000107) F17F8.3 SP [Arabidopsis thaliana] 456 18021 0 96 7262677 (AC012188) Contains similarity to SP MYB-Related Protein B from Gallus gallus g [Arabidopsis thaliana] 457 18245 1.00E−168 86 15239503 (NM_122484) GATA transcription SP factor - like [Arabidopsis thaliana] 458 18617 3.00E−69  94 18424873 (NM_125879) expressed protein SP [Arabidopsis thaliana] 459 18734 0 96 15237253 (NM_121609) UVB-resistance SP protein-like [Arabidopsis thaliana] 460 18823 0 82 15222227 AAM62510.1| (AY085278) homeodomain SP protein BELL1, putative [Arabidopsis thaliana] 461 19222 0 100 18390636 (NM_100509) expressed protein PP SP [Arabidopsis thaliana] 462 19430 0 95 18405149 (NM_129533) expressed protein SP [Arabidopsis thaliana] 463 12332 1.00E−113 84 15221408 (NM_106142) myb-related transcription SS activator, putative [Arabidopsis thaliana] 464 13649 1.00E−127 92 11281134 hypothetical protein F9G14.50 - SS Arabidopsis thaliana 465 16113 0 97 15217485 AAD18098.1| (AC006416) Identical to SS gb|Y10557 g5bf gene from Arabidopsis thaliana putative RNA-binding protein [Arabidopsis thaliana] 466 12069 1.00E−63  100 18410081 (NM_105902) expressed protein SS [Arabidopsis thaliana] 467 12906 0 98 5915825 Cytochrome P450 71B2 dbj|BAA28537.1| SS (D78605) cytochrome P450 monooxygenase [Arabidopsis thaliana] 468 13443 1.00E−111 100 18409105 (NM_114908) expressed protein SS [Arabidopsis thaliana] 469 14707 0 96 13122288 (AB047808) proteasel (pfpl)-like SS protein [Arabidopsis thaliana] 470 15116 1.00E−167 100 15242465 (NM_121002) inorganic pyrophosphatase - SS like protein [Arabidopsis thaliana] 471 16117 1.00E−90  78 15227349 (NM_129704) calmodulin-like protein SS [Arabidopsis thaliana] 472 16136 1.00E−115 92 15222919 (NM_101236) unknown protein SS [Arabidopsis thaliana] 473 19077 8.00E−98  70 15221874 (NM_101737) hypothetical protein HS PP SS [Arabidopsis thaliana] 474 19178 0 95 6321456 (NC_001139) gamma-aminobutyrate CK HS PEG PP SS (GABA) transaminase (4-aminobutyrate aminotransferase); Uga1p [Saccharomyces cerevisiae] 475 70752 4.00E−46  100 15224299 trypsin inhibitor-related SS [Arabidopsis thaliana] gi|3287862|sp|O22867|ITI5_ARATH 476 70753 4.00E−86  100 15231204 (NM_112176) DnaJ protein, putative SS [Arabidopsis thaliana] 477 70809 6.00E−70  48 20503004 (AC098693) Hypothetical protein LL PP SS [Oryza sativa (japonica cultivar-group)] 478 72091 1.00E−177 94 6322655 (NC_001143) Interacts with and may LL LN SS be a positive regulator of GLC7 which encodes type1 protein phosphatase; Sds22p [Saccharomyces cerevisiae]

Trait Improvement Screens

DS—Improvement of Drought Tolerance Identified by Soil Drought Stress Tolerance Screen:

Drought or water deficit conditions impose mainly osmotic stress on plants. Plants are particularly vulnerable to drought during the flowering stage. The drought condition in the screening process disclosed in Example 1B started from the flowering time and was sustained to the end of harvesting. The present invention provides recombinant DNA that can improve the plant survival rate under such sustained drought condition. Exemplary recombinant RNA for conferring such drought tolerance are identified as such in Table 3. Such recombinant RNA may find particular use in generating transgenic plants that are tolerant to the drought condition imposed during flowering time and in other stages of the plant life cycle. As demonstrated from the model plant screen, in some embodiments of transgenic plants with trait-improving recombinant DNA grown under such sustained drought condition can also have increased total seed weight per plant in addition to the increased survival rate within a transgenic population, providing a higher yield potential as compared to control plants.

PEG—Improvement of Drought Tolerance Identified by PEG Induced Osmotic Stress Tolerance Screen:

Various drought levels can be artificially induced by using various concentrations of polyethylene glycol (PEG) to produce different osmotic potentials (Pilon-Smits et a. (1995) Plant Physiol. 107:125-130). Several physiological characteristics have been reported as being reliable indications for selection of plants possessing drought tolerance. These characteristics include the rate of seed germination and seedling growth. The traits can be assayed relatively easily by measuring the growth rate of seedling in PEG solution. Thus, a PEG-induced osmotic stress tolerance screen is a useful surrogate for drought tolerance screen. As demonstrated from the model plant screen, embodiments of transgenic plants with trait-improving recombinant DNA identified in a PEG-induced osmotic stress tolerance screen can survive better drought conditions providing a higher yield potential as compared to control plants.

SS—Improvement of Drought Tolerance Identified by High Salinity Stress Tolerance Screen:

Three different factors are responsible for salt damages: (1) osmotic effects, (2) disturbances in the mineralization process, (3) toxic effects caused by the salt ions, e.g., inactivation of enzymes. While the first factor of salt stress results in the wilting of the plants that is similar to drought effect, the ionic aspect of salt stress is clearly distinct from drought. The present invention provides genes that help plants to maintain biomass, root growth, and/or plant development in high salinity conditions, which are identified as such in Table 3. Since osmotic effect is one of the major component of salt stress, which is common to the drought stress, trait-improving recombinant DNA identified in a high salinity stress tolerance screen can provide transgenic crops with improved drought tolerance.

HS—Improvement of Drought Tolerance Identified by Heat Stress Tolerance Screen:

Heat and drought stress often occur simultaneously, limiting plant growth. Heat stress can cause the reduction in photosynthesis rate, inhibition of leaf growth and osmotic potential in plants. Thus, genes identified by the present invention as heat stress tolerance conferring genes may also impart improved drought tolerance to plants.

CK and CS—Improvement of Tolerance to Cold Stress:

Low temperature may immediately result in mechanical constraints, changes in activities of macromolecules, and reduced osmotic potential. In the present invention, two screening conditions, i.e., cold shock tolerance screen (CK) and cold germination tolerance screen (CS), were set up to look for transgenic plants that display visual growth advantage at lower temperature. In cold germination tolerance screen, the transgenic Arabidopsis plants were exposed to a constant temperature of 8° C. from planting until day 28 post planting. The recombinant nucleotides identified by such screen as cold stress tolerance conferring genes are particular useful for the production of transgenic plant that can germinate more robustly in a cold temperature as compared to the wild type plants. In cold shock tolerance screen, the transgenic plants were first grown under the normal growth temperature of 22° C. until day 8 post planting, and subsequently were placed under 8° C. until day 28 post planting. In some preferred embodiments, transgenic plants transformed with the recombinant DNA constructs comprising SEQ ID NO: 1 or SEQ ID NO: 2 display more robust growth in both cold tolerance screens.

Improvement of Tolerance to Multiple Stresses:

Different kinds of stresses often lead to identical or similar reaction in the plants. Genes that are activated or inactivated as a reaction to stress can either act directly in a way the genetic product reduces a specific stress, or they can act indirectly by activating other specific stress genes. By manipulating the activity of such regulatory genes, i.e., multiple stress tolerance genes, the plant can be enabled to react to different kinds of stresses. For examples, SEQ ID NO: 37, SEQ ID NO: 38 and SEQ ID NO: 128 can be used to improve both heat stress tolerance and cold stress tolerance in plants. Of particular interest, plants transformed with SEQ ID NO: 59 can resist heat stress, salt stress and cold stress. In addition to these multiple stress tolerance genes, the stress tolerance conferring genes provided by the present invention may be used in combinations to generate transgenic plants that can resist multiple stress conditions.

PP—Improvement of Early Plant Growth and Development.

It has been known in the art that to minimize the impact of disease on crop profitability, it is important to start the season with healthy vigorous plants. This means avoiding seed and seedling diseases, leading to increased nutrient uptake and increased yield potential. Traditionally early planting and applying fertilizer are the methods used for promoting early seedling vigor. In early development stage, plant embryos establish only the basic root-shoot axis, a cotyledon storage organ(s), and stem cell populations, called the root and shoot apical meristems, which continuously generate new organs throughout post-embryonic development. “Early growth and development” used herein encompasses the stages of seed imbibition through the early vegetative phase. The present invention provides genes that are useful to produce transgenic plants that have advantages in one or more processes including, but not limited to, germination, seedling vigor, root growth and root morphology under non-stressed conditions. The transgenic plants starting from a more robust seedling are less susceptible to the fungal and bacterial pathogens that attach germinating seeds and seedling. Furthermore, seedlings with advantage in root growth are more resistant to drought stress due to extensive and deeper root architecture. Therefore, the genes conferring the growth advantage in early stages to plants may also be used to generate transgenic plants that are more resistant to various stress conditions due to improved early plant development. The present invention provides such exemplary genes that confer both the stress tolerance and growth advantages to plants, identified as such in Table 3, e.g., SEQ ID NO: 128 which can improve the plant early growth and development and impart heat and cold tolerance to plants.

SP—Improvement of Late Plant Growth and Development

“Late growth and development” used herein encompasses the stages of leaf development, flower production, and seed maturity. In certain embodiments, transgenic plants produced using genes that confer growth advantages to plants provided by the present invention, identified as such in Table 3, exhibit at least one phenotypic characteristics including, but not limited to, increased rosette radius, increased rosette dry weight, seed dry weight, silique dry weight, and silique length. On one hand, the rosette radius and rosette dry weight are used as the indexes of photosynthesis capacity, and thereby plant source strength and yield potential of a plant. On the other hand, the seed dry weight, silique dry weight and silique length are used as the indexes for plant sink strength, which are considered as the direct determinants of yield.

LL—Improvement of Tolerance to Shade Stress

The effects of light on plant development are especially prominent at the seedling stage. Under normal light conditions with unobstructed direct light, a plant seeding develops according to a characteristic photomorphogenic pattern, in which plants have open and expanded cotyledons and short hypocotyls. Then the plant's energy is devoted to cotyledon and leaf development while longitudinal extension growth is minimized. Under low light condition where light quality and intensity are reduced by shading, obstruction or high population density, a seedling displays a shade-avoidance pattern, in which the seedling displays a reduced cotyledon expansion, and hypocotyls extension is greatly increased. As the result, a plant under low light condition increases significantly its stem length at the expanse of leaf, seed or fruit and storage organ development, thereby adversely affecting of yield. The present invention provides recombinant nucleotides that enable plants to have an attenuated shade avoidance response so that the source of plant can be contribute to reproductive growth efficiently, resulting higher yield as compared to the wild type plants. One skilled in the art can recognize that transgenic plants generated by the present invention may be suitable for a higher density planting, thereby resulting increased yield per unit area. In some preferred embodiments, the present invention provides transgenic plants that have attenuated low light response and advantage in the flower bud formation.

LN—Improvement of Tolerance to Low Nitrogen Availability Stress

Nitrogen is a key factor in plant growth and crop yield. The metabolism, growth and development of plants are profoundly affected by their nitrogen supply. Restricted nitrogen supply alters shoot to root ratio, root development, activity of enzymes of primary metabolism and the rate of senescence (death) of older leaves. All field crops have a fundamental dependence on inorganic nitrogenous fertilizer. Since fertilizer is rapidly depleted from most soil types, it must be supplied to growing crops two or three times during the growing season. Improved nitrogen use efficiency by plants should enable crops cultivated under low nitrogen availability stress condition resulted from low fertilizer input or poor soil quality.

According to the present invention, transgenic plants generated using the recombinant nucleotides, which confer improved nitrogen use efficiency, identified as such in Table 3, exhibit one or more desirable traits including, but not limited to, increased seedling weight, increased number of green leaves, increased number of rosette leaves, increased root length and advanced flower bud formation. One skilled in the art may recognize that the transgenic plants with improved nitrogen use efficiency, established by the present invention may also have altered amino acid or protein compositions, increased yield and/or better seed quality. The transgenic plants of the present invention may be productively cultivated under nitrogen nutrient deficient conditions, i.e., nitrogen-poor soils and low nitrogen fertilizer inputs that would cause the growth of wild type plants to cease or to be so diminished as to make the wild type plants practically useless. The transgenic plants also may be advantageously used to achieve earlier maturing, faster growing, and/or higher yielding crops and/or produce more nutritious foods and animal feedstocks when cultivated using nitrogen non-limiting growth conditions.

Stacked Traits

The present invention also encompasses transgenic plants with stacked engineered traits, e.g., a crop having an improved phenotype resulting from expression of a trait-improving recombinant DNA, in combination with herbicide and/or pest resistance traits. For example, genes of the current invention can be stacked with other traits of agronomic interest, such as a trait providing herbicide resistance, for example a RoundUp Ready trait, or insect resistance, such as using a gene from Bacillus thuringensis to provide resistance against lepidopteran, coliopteran, homopteran, hemiopteran, and other insects. Herbicides for which resistance is useful in a plant include glyphosate herbicides, phosphinothricin herbicides, oxynil herbicides, imidazolinone herbicides, dinitroaniline herbicides, pyridine herbicides, sulfonylurea herbicides, bialaphos herbicides, sulfonamide herbicides and gluphosinate herbicides. To illustrate that the production of transgenic plants with herbicide resistance is a capability of those of ordinary skill in the art, reference is made to U.S. patent application publications 2003/0106096A1 and 2002/0112260A1 and U.S. Pat. Nos. 5,034,322; 5,776,760, 6,107,549 and 6,376,754, all of which are incorporated herein by reference. To illustrate that the production of transgenic plants with pest resistance is a capability of those of ordinary skill in the art reference is made to U.S. Pat. Nos. 5,250,515 and 5,880,275 which disclose plants expressing an endotoxin of Bacillus thuringiensis bacteria, to U.S. Pat. No. 6,506,599 which discloses control of invertebrates which feed on transgenic plants which express dsRNA for suppressing a target gene in the invertebrate, to U.S. Pat. No. 5,986,175 which discloses the control of viral pests by transgenic plants which express viral replicase, and to U.S. Patent Application Publication 2003/0150017 A1 which discloses control of pests by a transgenic plant which express a dsRNA targeted to suppressing a gene in the pest, all of which are incorporated herein by reference.

Once one recombinant DNA has been identified as conferring an improved trait of interest in transgenic Arabidopsis plants, several methods are available for using the sequence of that recombinant DNA and knowledge about the protein it encodes to identify homologs of that sequence from the same plant or different plant species or other organisms, e.g., bacteria and yeast. Thus, in one aspect, the invention provides methods for identifying a homologous gene with a DNA sequence homologous to any of SEQ ID NO: 1 through SEQ ID NO: 151 and SEQ ID NO: 153 through SEQ ID NO: 239, or a homologous protein with an amino acid sequence homologous to any of SEQ ID NO: 240 through SEQ ID NO: 390 and SEQ ID NO: 392 through SEQ ID NO: 478. In another aspect, the present invention provides the protein sequences of identified homologs for a sequence listed as SEQ ID NO: 240 through SEQ ID NO: 390 and SEQ ID NO: 392 through SEQ ID NO: 478. In yet another aspect, the present invention also includes linking or associating one or more desired traits, or gene function with a homolog sequence provided herein.

The trait-improving recombinant DNA and methods of using such trait-improving recombinant DNA for generating transgenic plants with improved traits provided by the present invention are not limited to any particular plant species. Indeed, the plants according to the present invention may be of any plant species, i.e., may be monocotyledonous or dicotyledonous. Preferably, they will be agricultural useful plants, i.e., plants cultivated by man for purposes of food production or technical, particularly industrial applications. Of particular interest in the present invention are corn and soybean plants. The recombinant DNA constructs optimized for soybean transformation and corn transformation are provide by the present invention. Other plants of interest in the present invention for production of transgenic plants having improved traits include, without limitation, cotton, canola, wheat, sunflower, sorghum, alfalfa, barley, millet, rice, tobacco, fruit and vegetable crops, and turfgrass.

In certain embodiments, the present invention contemplates to use an orthologous gene in generating the transgenic plants with similarly improved traits as the transgenic Arabidopsis counterpart. Improved physiological properties in transgenic plants of the present invention may be confirmed in responses to stress conditions, for example in assays using imposed stress conditions to detect improved responses to drought stress, nitrogen deficiency, cold growing conditions, or alternatively, under naturally present stress conditions, for example under field conditions. Biomass measures may be made on greenhouse or field grown plants and may include such measurements as plant height, stem diameter, root and shoot dry weights, and, for corn plants, ear length and diameter.

Trait data on morphological changes may be collected by visual observation during the process of plant regeneration as well as in regenerated plants transferred to soil. Such trait data includes characteristics such as normal plants, bushy plants, taller plants, thicker stalks, narrow leaves, striped leaves, knotted phenotype, chlorosis, albino, anthocyanin production, or altered tassels, ears or roots. Other improved traits may be identified by measurements taken under field conditions, such as days to pollen shed, days to silking, leaf extension rate, chlorophyll content, leaf temperature, stand, seedling vigor, internode length, plant height, leaf number, leaf area, tillering, brace roots, stay green, stalk lodging, root lodging, plant health, bareness/prolificacy, green snap, and pest resistance. In addition, trait characteristics of harvested grain may be confirmed, including number of kernels per row on the ear, number of rows of kernels on the ear, kernel abortion, kernel weight, kernel size, kernel density and physical grain quality.

To confirm hybrid yield in transgenic corn plants expressing genes of the present invention, it may be desirable to test hybrids over multiple years at multiple locations in a geographical location where maize is conventionally grown, e.g., in Iowa, Illinois or other locations in the midwestern United States, under “normal” field conditions as well as under stress conditions, e.g., under drought or population density stress.

Transgenic plants can be used to provide plant parts according to the invention for regeneration or tissue culture of cells or tissues containing the constructs described herein. Plant parts for these purposes can include leaves, stems, roots, flowers, tissues, epicotyl, meristems, hypocotyls, cotyledons, pollen, ovaries, cells and protoplasts, or any other portion of the plant which can be used to regenerate additional transgenic plants, cells, protoplasts or tissue culture. Seeds of transgenic plants are provided by this invention can be used to propagate more plants containing the trait-improving recombinant DNA constructs of this invention. These descendants are intended to be included in the scope of this invention if they contain a trait-improving recombinant DNA construct of this invention, whether or not these plants are selfed or crossed with different varieties of plants.

The various aspects of the invention are illustrated by means of the following examples which are in no way intended to limit the full breath and scope of claims.

EXAMPLES Example 1 Identification of Recombinant DNA that Confers Improved Trait(s) to Plants A. Expression Constructs for Arabidopsis Plant Transformation

Each gene of interest was amplified from a genomic or cDNA library using primer specific to sequences upstream and downstream of coding region. Transformation vectors were prepared to constitutively transcribe DNA in either sense orientation (for enhanced protein expression) or anti-sense orientation (for endogenous gene suppression) under the control of an enhanced Cauliflower Mosaic Virus 35S promoter (U.S. Pat. No. 5,359,142) directly or indirectly (Moore et al., PNAS 95:376-381, 1998; Guyer et al., Genetics 149: 633-639, 1998; International patent application NO. PCT/EP98/07577). The transformation vectors also contain a bar gene as a selectable marker for resistance to glufosinate herbicide. The transformation of Arabidopsis plants was carried out using the vacuum infiltration method known in the art (Bethtold et al., Methods Mol. Biol. 82:259-66, 1998). Seeds harvested from the plants, named as T1 seeds, were subsequently were grown in a glufosinate-containing selective medium to select for plants which were actually transformed and which produced T2 transgenic seed. For first pass screening T2 seeds from five independent transgenic lines of Arabidopsis were

B. Soil Drought Tolerance Screen

This example describes a soil drought tolerance screen to identify Arabidopsis plants transformed with recombinant DNA that wilt less rapidly and/or produce higher seed yield when grown in soil under drought conditions

T2 seeds were sown in flats filled with Metro/Mix® 200 (The Scotts® Company, USA). Humidity domes were added to each flat and flats were assigned locations and placed in climate-controlled growth chambers. Plants were grown under a temperature regime of 22° C. at day and 20° C. at night, with a photoperiod of 16 hours and average light intensity of 170 μmol/m²/s. After the first true leaves appeared, humidity domes were removed. The plants were sprayed with glufosinate herbicide and put back in the growth chamber for 3 additional days. Flats were watered for 1 hour the week following the herbicide treatment. Watering was continued every seven days until the flower bud primordia became apparent, at which time plants were watered for the last time.

To identify drought tolerant plants, plants were evaluated for wilting response and seed yield. Beginning ten days after the last watering, plants were examined daily until 4 plants/line had wilted. In the next six days, plants were monitored for wilting response. Five drought scores were assigned according to the visual inspection of the phenotypes: 1 for healthy, 2 for dark green, 3 for wilting, 4 severe wilting, and 5 for dead. A score of 3 or higher was considered as wilted.

At the end of this assay, seed yield measured as seed weight per plant under the drought condition was characterized for the transgenic plants and their controls and analyzed as a quantitative response according to example 1M.

Two approaches were used for statistical analysis on the wilting response. First, the risk score was analyzed for wilting phenotype and treated as a qualitative response according to the example 1L. Alternatively, the survival analysis was carried out in which the proportions of wilted and non-wilted transgenic and control plants were compared over each of the six days under scoring and an overall log rank test was performed to compare the two survival curves using S-PLUS statistical software (S-PLUS 6, Guide to statistics, Insightful, Seattle, Wash., USA). Table 4 provides a list of recombinant DNA constructs that improve drought tolerance in transgenic plants.

TABLE 4 Wilt Response Seed Weight/ Survival Anaysis Pep Risk score plant of wilt response SEQ Con- RS p- p- diff time p- ID struct_id Orientation mean value c delta value c to wilting value c 241 74518 SENSE −0.131 0.985 / 1.26 0 S 0 1 / 290 70222 SENSE −0.032 0.726 / 0.461 0.001 S −0.63 0.21 / 307 18280 SENSE −0.066 0.937 / 0.402 0.004 S 0 1 / 357 70247 SENSE 0.11 0.169 T 0.336 0.006 S −0.57 0.134 / 369 72471 SENSE 0.16 0.038 S −0.053 0.546 / 0.16 0.226 / 398 10188 ANTI-SENSE 0.133 0.004 S 0.68 0 S 0.24 0.297 / 399 10404 ANTI-SENSE 0.13 0.068 T 0.2 0.271 / 0.57 0.083 T 400 11333 ANTI-SENSE 0.266 0.007 S 0.291 0.293 / 0.77 0.131 T 401 11719 ANTI-SENSE 0.56 0.006 S −0.088 0.751 / 0 1 / 402 13663 ANTI-SENSE 0.123 0.024 S −0.198 0.763 / 0.04 0.852 / 403 13958 ANTI-SENSE 0.526 0.001 S 0.518 0.08 T 0 1 / 404 15214 ANTI-SENSE 0.018 0.208 / 0.19 0.243 / 0.06 0.815 / 405 10483 SENSE 0.313 0.012 S −0.095 0.795 / 0.28 0.358 / 406 11711 SENSE 0.346 0.005 S 0.218 0.009 S 0.3 0.371 / 407 11909 SENSE 0.094 0.021 S 0.002 0.493 / 0.26 0.767 / 408 12216 SENSE 0.623 0 S −0.195 0.714 / 2.55 0.007 S 409 12236 SENSE 0.233 0.019 S 0.32 0.026 S 0.29 0.124 T 410 12256 SENSE 0.254 0.001 S 0.133 0.245 / 0.09 0.869 / 411 12806 SENSE 0.198 0.016 S 0.689 0.018 S 0.16 0.696 / 412 12904 SENSE 0.292 0.033 S −1.195 0.992 / 0.81 0.023 S 413 13212 SENSE 0.24 0.006 S 0.676 0.01 S 0.25 0.559 / 414 13232 SENSE 0.166 0.134 T −0.044 0.568 / 0.81 0.105 T 415 13912 SENSE 0.3 0 S −0.084 0.74 / 0.91 0.054 T 416 14327 SENSE 0.181 0.008 S −0.423 0.831 / 0.75 0.021 S 417 14704 SENSE 0.174 0.01 S 0.26 0.003 S 0.92 0.538 / 418 14714 SENSE 0.313 0.007 S −0.283 0.987 / 0.3 0.702 / 419 15142 SENSE 0.28 0 S −0.498 0.871 / 0.29 0.196 T 420 17450 SENSE 0.117 0.102 T 0.238 0.079 T −0.05 0.834 / 421 18607 SENSE 0.161 0.013 S −0.167 0.782 / 0.64 0.034 S 422 19409 SENSE 0.177 0.032 S 0.33 0.119 T 0.36 0.298 / 423 19412 SENSE 0.501 0.001 S −0.006 0.515 / 0.15 0.84 / S: represents that the transgenic plants showed statistically significant trait improvement as compared to the reference (p < 0.05, p value, of the delta of a quantitative response or of the risk score of a qualitative response, is the probability that the observed difference between the transgenic plants and the reference occur by chance) T: represents that the transgenic plants showed a trend of trait improvement as compared to the reference, preferably with p < 0.2, /: represents the transgenic plants didn't show any alteration or had unfavorable change in traits examined compared to the reference in the current dataset.

C. Heat Stress Tolerance Screen

Under high temperatures, Arabidopsis seedlings become chlorotic and root growth is inhibited. This example sets forth the heat stress tolerance screen to identify Arabidopsis plants transformed with the gene of interest that are more resistant to heat stress based on primarily their seedling weight and root growth under high temperature. T2 seeds were plated on ½×MS salts, 1% phytagel, with 10 μg/ml glufosinate (7 per plate with 2 control seeds; 9 seeds total per plate). Plates were placed at 4° C. for 3 days to stratify seeds. Plates were then incubated at room temperature for 3 hours and then held vertically for 11 additional days at temperature of 34° C. at day and 20° C. at night. Photoperiod was 16 h. Average light intensity was ˜140 μmol/m²/s. After 14 days of growth, plants were scored for glufosinate resistance, root length, final growth stage, visual color, and seedling fresh weight. A photograph of the whole plate was taken on day 14.

Visual assessment was carried out to evaluate the robustness of the growth based on the leave size and rosette size.

The seedling weight and root length were analyzed as quantitative responses according to example 1M. The final grow stage at day 14 was scored as success if 50% of the plants had reached 3 rosette leaves and size of leaves are greater than 1 mm (Boyes, et al., (2001) The Plant Cell 13, 1499-1510). The growth stage data was analyzed as a qualitative response according to example 1L. Table 5 provides a list of recombinant DNA constructs that improve heat tolerance in transgenic plants.

TABLE 5 Pep seedling weight Root Length growth stage SEQ Con- p- p- RS p- ID struct_id Orientation delta value c delta value c mean value c 268 12007 ANTI-SENSE 1.283 0 S 0.221 0.018 S 0.844 0.044 S 269 12290 ANTI-SENSE 0.92 0.002 S −0.09 0.683 / 0.4 0.14 T 270 12343 ANTI-SENSE 1.186 0 S 0.008 0.478 / −0.066 0.818 / 271 14348 ANTI-SENSE 0.917 0 S 0.047 0.352 / 0.034 0.314 / 272 15708 ANTI-SENSE 1.12 0 S 0.122 0.092 T 0.467 0.016 S 273 17615 ANTI-SENSE 1.134 0 S 0.176 0.084 T 0.541 0.102 T 274 17622 ANTI-SENSE 0.728 0 S −0.142 0.874 / 0.875 0.002 S 275 70714 ANTI-SENSE 1.029 0 S 0.032 0.355 / −0.003 0.515 / 276 17925 SENSE 0.969 0 S −0.027 0.588 / 0.22 0.215 / 277 18541 SENSE 0.977 0 S −0.012 0.559 / 0.982 0.028 S 278 11425 SENSE 1.255 0 S 0.152 0.096 T 0.516 0.005 S 279 12263 SENSE 0.869 0.003 S −0.023 0.552 / 0.481 0.113 T 280 12288 ANTI-SENSE 1.256 0 S 0.086 0.314 / 0.968 0.036 S 281 12910 SENSE 1.067 0.105 T 0.097 0.274 / −0.417 1 / 282 14335 SENSE 1.107 0 S 0.16 0 S −0.024 0.804 / 283 17427 SENSE 0.837 0 S −0.069 0.706 / 0.569 0.087 T 284 19140 SENSE 0.894 0 S 0.111 0.131 T 1.794 0 S 285 19179 SENSE 1.039 0 S −0.095 0.742 / 0.614 0.063 T 286 19251 SENSE 0.77 0 S −0.061 0.771 / 0.543 0.027 S 287 19443 SENSE 1.115 0 S 0.042 0.369 / 0.537 0.078 T 288 19607 SENSE 0.939 0 S 0.024 0.381 / 0.095 0.215 / 289 19915 SENSE 1.336 0.057 T 0.19 0.299 / 0.07 0 S 290 70222 SENSE 0.778 0.004 S −0.078 0.677 / 1.153 0.015 S 291 70464 SENSE 1.039 0 S 0.026 0.411 / 0.806 0.04 S 292 70474 SENSE 1.026 0 S 0.094 0.207 / 1.145 0.03 S 293 70484 SENSE 1.511 0 S 0.236 0.004 S 0.688 0.016 S 294 72474 SENSE 0.816 0 S 0.095 0.229 / 1.149 0.01 S 298 19252 SENSE 0.571 0.111 T 0.02 0.416 / 1.27 0.022 S 347 18854 SENSE 0.854 0 S −0.14 0.896 / 0.595 0.148 T 351 16226 SENSE 1.372 0 S 0.244 0.009 S 0.112 0.017 S 357 70247 SENSE 1.146 0 S 0.124 0.114 T 0.953 0.029 S 359 12635 SENSE 0.702 0.109 T 0.587 0.001 S 0.637 0.06 T 367 14338 SENSE 0.888 0 S 0.036 0.326 / 0.17 0.077 T 368 17809 SENSE 0.838 0.002 S 0.033 0.308 / 0.619 0.04 S 369 72471 SENSE 1.051 0.001 S 0.067 0.227 / 1.531 0.005 S 373 72772 SENSE 1.364 0 S 0.299 0.002 S 0.648 0.045 S 395 70202 SENSE 1.159 0 S −0.116 0.941 / 0.339 0.159 T 435 19719 SENSE 1.184 0 S 0.032 0.411 / 1.433 0.018 S 473 19077 SENSE 1.405 0 S 0.026 0.369 / 0.61 0.013 S 474 19178 SENSE 1.381 0 S 0.267 0.008 S 1.54 0.006 S S: represents the transgenic plants showed statistically significant trait improvement as compared to the reference (p < 0.05) T: represents the transgenic plants showed a trend of trait improvement as compared to the reference, preferably with p < 0.2 /: represents the transgenic plants didn't show any alteration or had unfavorable change in traits examined compared to the reference in the current dataset

D. Salt Stress Tolerance Screen

This example sets forth the high salinity stress screen to identify Arabidopsis plants transformed with the gene of interest that are tolerant to high levels of salt based on their rate of development, root growth and chlorophyll accumulation under high salt conditions.

T2 seeds were plated on glufosinate selection plates containing 90 mM NaCl and grown under standard light and temperature conditions. All seedlings used in the experiment were grown at a temperature of 22° C. at day and 20° C. at night, a 16-hour photoperiod, an average light intensity of approximately 120 umol/m². On day 11, plants were measured for primary root length. After 3 more days of growth (day 14), plants were scored for transgenic status, primary root length, growth stage, visual color, and the seedlings were pooled for fresh weight measurement. A photograph of the whole plate was also taken on day 14.

Visual assessment was carried out to evaluate the robustness of the growth based on the leave size and rosette size.

The seedling weight and root length were analyzed as quantitative responses according to example 1M. The final growth stage at day 14 was scored as success if 50% of the plants reached 3 rosette leaves and size of leaves are greater than 1 mm (Boyes, D. C., et al., (2001), The Plant Cell 13, 1499/1510). The growth stage data was analyzed as a qualitative response according to example 1L.

TABLE 6 a list of recombinant nucleotides that improve high salinity tolerance in plants Seedling Weight Root Length Root Length Pep Con- at day 14 at day 11 at day 14 Growth Stage SEQ struct p- p- p- RS p- ID id delta value c delta value c delta vallue c mean value c 243 17918 0.749 0.001 S 0.007 0.945 / 0.054 0.348 / 0.107 0.152 T 258 17819 0.713 0.026 S 0.281 0.09 T 0.29 0.01 S 1.565 0.025 S 285 19179 0.939 0 S 0.228 0.044 S 0.269 0.001 S 1.561 0.034 S 298 19252 0.831 0.003 S 0.327 0.016 S 0.334 0.001 S 1.5 0.028 S 312 70405 0.266 0.096 T 0.051 0.628 / 0.202 0.014 S −0.201 0.766 / 372 18395 0.506 0.008 S 0.27 0.033 S 0.24 0.007 S 0.653 0.016 S 376 11409 0.834 0.004 S 0.305 0.007 S 0.329 0.001 S 0.712 0.073 T 390 18392 0.767 0 S 0.325 0.005 S 0.181 0.034 S 0.698 0.109 T 424 13005 0.787 0.003 S 0.228 0.021 S 0.161 0.12 T 1.079 0.013 S 439 18513 0.779 0.019 S 0.377 0.013 S 0.298 0.002 S 0.679 0.069 T 463 12332 0.292 0.604 / 0.204 0.22 / 0.057 0.829 / 0.538 0.188 T 464 13649 0.418 0.03 S 0.062 0.493 / 0.147 0.1 T 1.39 0.028 S 465 16113 0.108 0.305 / 0.168 0.221 / 0.138 0.076 T 1.09 0.068 T 466 12069 0.708 0.043 S 0.162 0.091 T 0.165 0.354 / 0.306 0.074 T 467 12906 0.764 0.05 T 0.185 0.039 S 0.175 0.01 S 1.212 0.009 S 468 13443 0.113 0.629 / −0.061 0.542 / −0.001 0.993 / 0.658 0.096 T 469 14707 0.388 0.159 T 0.088 0.452 / −0.094 0.564 / 0.366 0.012 S 470 15116 0.576 0.02 S 0.362 0.01 S 0.221 0.063 T 1.414 0.027 S 471 16117 0.038 0.789 / 0.02 0.87 / −0.003 0.98 / 0.599 0.224 / 472 16136 0.465 0.001 S 0.297 0 S 0.172 0.007 S 1.911 0.005 S 473 19077 0.525 0.02 S 0.23 0.006 S 0.214 0 S 0.299 0.116 T 474 19178 0.398 0.22 / 0.231 0.106 T 0.219 0.046 S 0.456 0.213 / 475 70752 0.273 0.379 / 0.122 0.387 / 0.096 0.417 / −0.022 0.519 / 476 70753 0.21 0.459 / −0.015 0.864 / 0.116 0.286 / 0.489 0.128 T 477 70809 0.802 0.007 S 0.233 0 S 0.348 0 S 2.24 0.009 S 478 72091 0.608 0.014 S 0.115 0.249 / 0.152 0.091 T 0.398 0.267 / S: represents the transgenic plants showed statistically significant trait improvement as compared to the reference (p < 0.05) T: represents the transgenic plants showed a trend of trait improvement as compared to the reference, preferably with p < 0.2 /: represents the transgenic plants didn't show any alteration or had unfavorable change in traits examined compared to the reference in the current dataset

E. Polyethylene Glycol (PEG) Induced Osmotic Stress Tolerance Screen

There are numerous factors, which can influence seed germination and subsequent seedling growth, one being the availability of water. Genes, which can directly affect the success rate of germination and early seedling growth, are potentially useful agronomic traits for improving the germination and growth of crop plants under drought stress. In this assay, PEG was used to induce osmotic stress on germinating transgenic lines of Arabidopsis thaliana seeds in order to screen for osmotically resistant seed lines.

T2 seeds were plated on glufosinate selection plates containing 3% PEG and grown under standard light and temperature conditions. Seeds were plated on each plate containing 3% PEG, ½ ×MS salts, 1% phytagel, and 10 μg/ml glufosinate. Plates were placed at 4° C. for 3 days to stratify seeds. On day 11, plants were measured for primary root length. After 3 more days of growth, i.e., at day 14, plants were scored for transgenic status, primary root length, growth stage, visual color, and the seedlings were pooled for fresh weight measurement. A photograph of the whole plate was taken on day 14. Visual assessment was carried out to evaluate the robustness of the growth based on the leave size and rosette size.

Seedling weight and root length were analyzed as quantitative responses according to example 1M. The final growth stage at day 14 was scored as success or failure based on whether the plants reached 3 rosette leaves and size of leaves are greater than 1 mm. The growth stage data was analyzed as a qualitative response according to example 1L.

TABLE 7 a list of recombinant nucleotides that improve osmotic stress tolerance in plants Seedling Weight Root Length Root Length Pep at day 14 at day 11 at day 14 Growth Stage SEQ Con- p- p- p- RS p- ID struct delta value c delta value c delta value c mean value c 241 74518 0.53 0.018 S 0.217 0.024 S 0.51 0.001 S 4 0 S 345 14825 0.414 0.181 T 0.271 0.053 T 0.102 0.34 / 2.105 0.01 S 346 17931 0.295 0.425 / 0.124 0.574 / 0.116 0.454 / 2.069 0.085 T 347 18854 0.484 0.015 S 0.342 0.011 S 0.159 0.073 T 1.023 0.238 / 348 12237 0.371 0.165 T 0.325 0.001 S 0.297 0.003 S 2.191 0.017 S 349 13414 0.137 0.311 / 0.241 0.069 T 0.265 0.045 S 2.461 0.027 S 350 16160 0.303 0.044 S 0.242 0.035 S 0.077 0.512 / 3.381 0.001 S 351 16226 0.367 0.047 S 0.132 0.224 / 0.097 0.276 / 4 0 S 352 16803 0.382 0.036 S 0.125 0.489 / 0.224 0.023 S 4 0 S 353 18260 0.183 0.315 / 0.125 0.315 / 0.146 0.143 T 3.362 0.002 S 354 18642 0.076 0.674 / 0.199 0.09 T 0.199 0.029 S 3.056 0.002 S 355 18721 0.336 0.104 T 0.177 0.145 T 0.109 0.228 / 2.281 0.02 S 356 19254 0.334 0.242 / 0.155 0.227 / 0.153 0.183 T 0.905 0.129 T 357 70247 0.45 0.138 T 0.334 0.008 S 0.169 0.07 T 2.692 0.013 S 358 70650 0.215 0.121 T 0.105 0.114 T 0.092 0.255 / 2.749 0.011 S 374 19441 0.413 0.017 S 0.256 0.003 S 0.098 0.085 T 2.324 0.04 S 424 13005 0.685 0.008 S 0.395 0.002 S 0.226 0.013 S 3.787 0 S 435 19719 0.306 0.04 S 0.135 0.051 T −0.028 0.426 / −0.338 0.598 / 474 19178 0.515 0.02 S 0.21 0.059 T 0.169 0.08 T 3.53 0 S S: represents the transgenic plants showed statistically significant trait improvement as compared to the reference (p < 0.05) T: represents the transgenic plants showed a trend of trait improvement compared to the reference, preferably with p < 0.2 /: represents the transgenic plants didn't show any alteration or had unfavorable change in traits examined compared to the reference in the current dataset

F. Cold Shock Tolerance Screen

This example set forth a screen to identify Arabidopsis plants transformed with the genes of interest that are more tolerant to cold stress subjected during day 8 to day 28 after seed planting. During these crucial early stages, seedling growth and leaf area increase were measured to assess tolerance when Arabidopsis seedlings were exposed to low temperatures. Using this screen, genetic alterations can be found that enable plants to germinate and grow better than wild type plants under sudden exposure to low temperatures.

T2 seeds were tested. Eleven seedlings from each line plus one control line were plated together on a plate containing ½ × Gamborg Salts with 0.8 Phytagel™, 1% Phytagel, and 0.3% Sucrose. Plates were then oriented horizontally and stratified for three days at 4° C. At day three, plates were removed from stratification and exposed to standard conditions (16 hr photoperiod, 22° C. at day and 20° C. at night) until day 8. At day eight, plates were removed from standard conditions and exposed to cold shock conditions (24 hr photoperiod, 8° C. at both day and night) until the final day of the assay, i.e., day 28. Rosette areas were measured at day 8 and day 28, which were analyzed as quantitative responses according to example 1M.

TABLE 8 a list of recombinant nucleotides that improve cold shock stress tolerance in plants difference in rosette area rosette area rosette area between day 28 Pep at day 8 at day 28 and day 8 SEQ Con- p- p- p- ID struct_id Orientation delta value c delta value c delta value c 240 19867 SENSE −0.032 0.603 / 0.15 0.309 / 0.426 0.064 T 241 74518 SENSE 0.184 0.192 T 0.653 0.001 S 0.796 0 S 242 15816 SENSE 0.366 0.027 S 0.592 0.002 S 0.666 0.004 S 243 17918 SENSE 0.594 0 S 0.982 0 S 1.325 0 S 276 17925 SENSE 0.479 0.001 S 0.693 0 S 0.872 0 S 474 19178 SENSE 0.23 0.083 T 0.435 0.026 S 0.435 0.103 T S: represents the transgenic plants showed statistically significant trait improvement as compared to the reference (p < 0.05) T: represents the transgenic plants showed a trend of trait improvement compared to the reference, preferably with p < 0.2 /: represents the transgenic plants didn't show any alteration or had unfavorable change in traits examined compared to the reference in the current dataset.

G. Cold Germination Tolerance Screen

This example sets forth a screen to identify Arabidopsis plants transformed with the genes of interests are resistant to cold stress based on their rate of development, root growth and chlorophyll accumulation under low temperature conditions.

T2 seeds were plated and all seedlings used in the experiment were grown at 8° C. Seeds were first surface disinfested using chlorine gas and then seeded on assay plates containing an aqueous solution of ½ × Gamborg's B/5 Basal Salt Mixture (Sigma/Aldrich Corp., St. Louis, Mo., USA G/5788), 1% Phytagel™ (Sigma-Aldrich, P-8169), and 10 ug/ml BASTA™ (Bayer Crop Science, Frankfort, Germany), with the final pH adjusted to 5.8 using KOH. Test plates were held vertically for 28 days at a constant temperature of 8° C., a photoperiod of 16 hr, and average light intensity of approximately 100 umol/m²/s. At 28 days post planting, root length was measured, growth stage was observed, the visual color was assessed, and a whole plate photograph was taken.

Visual assessment was carried out to evaluate the robustness of the growth based on the leave size and rosette size.

The root length at day 28 was analyzed as a quantitative response according to example 1M. The growth stage at day 7 was analyzed as a qualitative response according to example 1L.

TABLE 9 a list of recombinant nucleotides that improve cold stress tolerance in plants Root Length Growth Stage Pep at day 28 at day 28 SEQ Con- p- RS p- ID struct_id Orientation delta value c mean value c 240 19867 SENSE 0.071 0.292 / 1.954 0.103 T 241 74518 SENSE 0.278 0.031 S 4 0 S 244 15306 ANTI-SENSE 0.176 0.142 T 1.582 0.067 T 245 12038 SENSE 0.045 0.188 T 2.271 0.022 S 246 12046 SENSE 0.177 0.125 T 3.513 0 S 247 13432 SENSE 0.182 0.015 S 1.108 0.078 T 248 13711 SENSE 0.15 0.022 S 2.357 0.012 S 249 14809 SENSE −0.034 0.631 / 1.95 0.047 S 250 14951 SENSE 0.237 0.053 T 3.387 0.001 S 251 15632 SENSE 0.003 0.481 / 0.49 0.275 / 252 16147 SENSE 0.176 0.016 S 3.284 0.003 S 253 16158 SENSE 0.084 0.235 / 1.432 0.138 T 254 16170 SENSE 0.066 0.354 / 1.995 0.088 T 255 16171 SENSE −0.178 0.842 / −0.671 0.732 / 256 16175 SENSE −0.054 0.7 / 1.231 0.184 T 257 17430 SENSE 0.254 0.135 T 2.776 0.009 S 258 17819 SENSE 0.221 0.028 S −0.475 0.922 / 259 17921 SENSE −0.151 0.912 / 1.291 0.179 T 260 17928 SENSE 0.368 0.028 S 2.599 0.003 S 261 18637 SENSE 0.158 0.225 / 1.143 0.164 T 262 18816 SENSE 0.206 0.075 T 3.038 0.002 S 263 19227 SENSE 0.198 0.058 T 3.068 0.002 S 264 19429 SENSE 0.258 0.062 T 2.582 0.006 S 265 70235 SENSE 0.175 0.065 T 2.584 0.006 S 266 72634 SENSE 0.169 0.064 T 2.835 0.001 S 267 72752 SENSE 0.292 0.019 S 2.816 0.002 S 273 17615 ANTI-SENSE 0.317 0.006 S 2.239 0.022 S 277 18541 SENSE 0.321 0.072 T 2.631 0.014 S 293 70484 SENSE 0.2 0.018 S 2.61 0.016 S 298 19252 SENSE 0.391 0.002 S 1.041 0.084 T 346 17931 SENSE 0.096 0.059 T 1.213 0.142 T 357 70247 SENSE 0.299 0.006 S 2.607 0.005 S 366 19610 SENSE 0.33 0.079 T 4 0 S 367 14338 SENSE 0.223 0.071 T 1.125 0.087 T 376 11409 SENSE 0.193 0 S 1.831 0.024 S 434 17922 SENSE 0.238 0.029 S 3.109 0.002 S S: represents the transgenic plants showed statistically significant trait improvement as compared to the reference (p < 0.05) T: represents the transgenic plants showed a trend of trait improvement as compared to the reference, preferably with p < 0.2 /: represents the transgenic plants didn't show any alteration or had unfavorable change in traits examined compared to the reference in the current dataset

H. Shade Tolerance-Low Light Screen

Plants undergo a characteristic morphological response in shade that includes the elongation of the petiole, a change in the leaf angle, and a reduction in chlorophyll content. While these changes may confer a competitive advantage to individuals, in a monoculture the shade avoidance response is thought to reduce the overall biomass of the population. Thus, genetic alterations that prevent the shade avoidance response may be associated with higher yields. Genes that favor growth under low light conditions may also promote yield, as inadequate light levels frequently limit yield. This protocol describes a screen to look for Arabidopsis plants that show an attenuated shade avoidance response and/or grow better than control plants under low light intensity. Of particular interest, we were looking for plants that didn't extend their petiole length, had an increase in seedling weight relative to the reference and had leaves that were more close to parallel with the plate surface.

T2 seeds were plated on glufosinate selection plates with ½ MS medium. Seeds were sown on ½ ×MS salts, 1% Phytagel, 10 ug/ml BASTA. Plants were grown on vertical plates at a temperature of 22° C. at day, 20° C. at night and under low light (approximately 30 uE/m²/s, far/red ratio (655/665/725/735) ˜0.35 using PLAQ lights with GAM color filter #680). Twenty-three days after seedlings were sown, measurements were recorded including seedling status, number of rosette leaves, status of flower bud, petiole leaf angle, petiole length, and pooled fresh weights. A digital image of the whole plate was taken on the measurement day. Seedling weight and petiole length were analyzed as quantitative responses according to example 1M. The number of rosette leaves, flowering bud formation and leaf angel were analyzed as qualitative responses according to example 1L.

TABLE 10 a list of recombinant nucleotides that improve shade tolerance in plants flowerbud Number of formation leaf angle petiole length rosette leaves seedling weight Pep at day 23 at day 23 at day 23 at day 23 at day 23 SEQ Con- RS p- RS p- p- RS p- p- ID struct_id mean value c mean value c delta value c mean value c delta value c 262 18816 3.007 0.003 S 0.738 0.003 S 0.046 0.561 / −0.383 0.929 / 0.171 0.011 S 282 14335 1.81 0.029 S 0.404 0.032 S 0.204 0.301 / −0.043 0.814 / 0.39 0.093 T 295 13047 2.261 0.006 S 0.482 0.106 T −0.097 0.31 / 1.655 0.088 T 0.463 0.022 S 296 13304 −0.118 0.643 / −0.164 0.861 / −0.228 0.106 T 1.214 0.068 T 0.244 0.421 / 297 13474 −0.319 0.583 / 0.419 0.062 T −0.051 0.153 T 0.633 0.032 S 0.223 0.002 S 298 19252 −2 0.962 / 0.239 0.257 / 0.099 0.242 / 1.153 0.056 T 0.497 0 S 299 12612 −0.627 0.975 / −0.094 0.766 / −0.037 0.341 / 0.61 0.092 T −0.304 0.298 / 300 12926 0.827 0.15 T −0.278 1 / −0.02 0.51 / 0.489 0.218 / −0.374 0.279 / 301 13230 −0.228 0.954 / −0.05 0.668 / 0.057 0.33 / 1.83 0.025 S 0.33 0.124 T 302 14235 −0.511 1 / 0.084 0.271 / −0.324 0.045 S −0.205 0.848 / −0.536 0.016 / 303 17305 0.056 0.374 / 0.036 0.226 / −0.055 0.59 / 0.788 0.143 T −0.058 0.761 / 304 17470 0.319 0.344 / 0.231 0.112 T −0.218 0.24 / 1.314 0.052 T 0.094 0.612 / 305 17718 −1.438 0.985 / 0.005 0.486 / −0.148 0.016 S 1.793 0.027 S 0.033 0.728 / 306 17904 0.965 0.105 T 0.252 0.071 T −0.15 0.359 / 1.01 0.027 S −0.022 0.844 / 307 18280 −0.176 0.626 / 0.284 0.258 / −0.056 0.547 / 1.35 0.037 S 0.269 0.086 T 308 18287 −2.441 0.941 / 0.078 0.348 / −0.022 0.785 / 1.193 0.05 T 0.292 0.056 T 309 18501 −0.087 1 / −0.326 1 / −0.254 0.05 T 0.23 0.438 / −0.303 0.789 / 310 18877 0.181 0.414 / 0.016 0.41 / −0.119 0.372 / 0.351 0.212 / 0.076 0.604 / 311 19531 4 0 S 0.04 0.379 / −0.142 0.344 / −0.253 0.809 / 0.001 0.998 / 312 70405 −0.931 0.991 / −0.114 0.957 / −0.186 0.038 S 0.674 0.188 T 0.13 0.177 T 313 72136 −1.001 1 / 1.063 0.08 T −0.621 0.008 S 0.775 0.014 S −1.081 0.018 / 314 72611 −0.476 0.834 / 0.868 0.121 T −0.262 0.102 T 1.728 0.044 S −0.365 0.23 / 370 16403 2.223 0.01 S 0.132 0.144 T −0.157 0.484 / −1.052 0.999 / 0.148 0.766 / 427 12018 1.283 0.059 T 0.309 0.254 / −0.006 0.959 / 0.663 0.14 T −0.643 0.017 / 434 17922 1.171 0.136 T −0.046 0.58 / 0.057 0.624 / −0.042 0.614 / 0.317 0.056 T 436 17336 −0.987 1 / −0.297 1 / −0.11 0.079 T 1.082 0.074 T −0.121 0.636 / 437 17735 −3.705 1 / −0.016 0.524 / −0.135 0.084 T 0.882 0.022 S 0.014 0.9 / 477 70809 −1.333 0.913 / 0.184 0.173 T 0.102 0.256 / 0.236 0.148 T 0.449 0.046 S 478 72091 1.908 0.006 S 0.009 0.422 / 0.251 0.004 / −0.056 1 / 0.413 0.083 T S: represents the transgenic plants showed statistically significant trait improvement as compared to the reference (p < 0.05) T: represents the transgenic plants showed a trend of trait improvement as compared to the reference, preferably with p < 0.2 /: represents the transgenic plants didn't show any alteration or had unfavorable change in traits examined compared to the reference in the current dataset.

I. Early Plant Growth and Development Screen

This example sets forth a plate based phenotypic analysis platform for the rapid detection of phenotypes that are evident during the first two weeks of growth. In this screen, we were looking for genes that confer advantages in the processes of germination, seedling vigor, root growth and root morphology under non-stressed growth conditions to plants. The transgenic plants with advantages in seedling growth and development were determined by the seedling weight and root length at day 14 after seed planting.

T2 seeds were plated on glufosinate selection plates and grown under standard conditions (˜100 uE/m²/s, 16 h photoperiod, 22° C. at day, 20° C. at night). Seeds were stratified for 3 days at 4° C. Seedlings were grown vertically (at a temperature of 22° C. at day 20° C. at night). Observations were taken on day 10 and day 14. Both seedling weight and root length at day 14 were analyzed as quantitative responses according to example 1M.

TABLE 11 a list recombinant nucleotides that improve early plant growth and development Root Length Seedling Weight Pep at day 14 at day 14 SEQ Con- p- p- ID struct_id Orientation delta value c delta value c 241 74518 SENSE 0.216 0.01 S 0.454 0.049 S 245 12038 SENSE 0.101 0.046 S 0.629 0.003 S 250 14951 SENSE 0.15 0.072 T 0.138 0.378 / 260 17928 SENSE 0.062 0.22 / 0.246 0.069 T 265 70235 SENSE 0.079 0.519 / 0.414 0.026 S 267 72752 SENSE 0.301 0.001 S 0.789 0.002 S 285 19179 SENSE 0.216 0.024 S 0.603 0.01 S 290 70222 SENSE 0.047 0.468 / 0.394 0.014 S 293 70484 SENSE 0.068 0.364 / 0.444 0.024 S 294 72474 SENSE 0.241 0.051 T 0.183 0.564 / 298 19252 SENSE 0.065 0.392 / 0.316 0.054 T 326 17344 SENSE 0.042 0.565 / 0.223 0.066 T 330 17906 SENSE 0.11 0.152 T 0.419 0.011 S 354 18642 SENSE 0.1 0.247 / 0.257 0.043 S 357 70247 SENSE −0.04 0.842 / 0.237 0.134 T 358 70650 SENSE 0.121 0.077 T 0.135 0.442 / 359 11787 ANTI-SENSE −0.083 0.784 / 0.167 0.365 / 360 13641 ANTI-SENSE 0.092 0.15 T 0.336 0.053 T 361 14515 ANTI-SENSE 0.051 0.616 / 0.351 0.038 S 362 14920 ANTI-SENSE 0.08 0.358 / 0.101 0.739 / 363 15204 ANTI-SENSE 0.203 0.015 S 0.076 0.811 / 364 15216 ANTI-SENSE 0.316 0.023 S 0.632 0.073 T 365 15330 ANTI-SENSE 0.084 0.428 / 0.435 0.002 S 366 19610 SENSE 0.192 0.011 S 0.523 0.008 S 367 14338 SENSE 0.145 0.155 T 0.589 0.072 T 368 17809 SENSE 0.014 0.928 / −0.121 0.753 / 369 72471 SENSE 0.07 0.023 S 0.407 0.048 S 370 16403 SENSE 0.199 0.027 S 0.6 0.003 S 371 17737 SENSE 0.049 0.472 / 0.242 0.073 T 372 18395 SENSE 0.219 0.001 S 0.58 0.002 S 373 72772 SENSE 0.224 0.023 S 0.442 0.106 T 374 19441 SENSE 0.271 0 S 0.482 0.019 S 375 10486 SENSE 0.191 0.03 S 0.343 0.052 T 376 11409 SENSE 0.258 0.034 S 0.468 0.006 S 377 12104 SENSE 0.1 0.379 / 0.489 0.009 S 378 12258 SENSE 0.16 0.05 T 0.392 0.137 T 379 12909 SENSE 0.139 0.267 / 0.322 0.261 / 380 14310 SENSE 0.544 0 S 0.764 0.026 S 381 14317 SENSE 0.134 0.18 T 0.117 0.64 / 382 14709 SENSE 0.206 0.009 S 0.389 0.117 T 383 15123 SENSE 0.026 0.872 / 0.27 0.348 / 384 16013 SENSE 0.046 0.622 / 0.464 0.01 S 385 16185 SENSE 0.191 0.045 S 0.145 0.596 / 386 16719 SENSE 0.019 0.872 / 0.424 0.088 T 387 17490 SENSE 0.186 0.026 S 0.272 0.102 T 388 17905 SENSE 0.239 0.004 S 0.346 0.196 T 389 18385 SENSE 0.287 0.003 S 0.687 0.003 S 390 18392 SENSE 0.088 0.338 / 0.504 0.012 S 392 18531 SENSE 0.313 0.015 S 0.627 0 S 393 18603 SENSE 0.212 0 S 0.165 0.187 T 394 19530 SENSE 0.106 0.137 T 0.342 0.025 S 395 70202 SENSE 0.218 0.056 T 0.279 0.223 / 396 72009 SENSE 0.191 0.054 T 0.328 0.043 S 397 72119 SENSE 0.236 0 S 0.259 0.008 S 438 19249 SENSE 0.054 0.375 / 0.222 0.048 S 439 18513 SENSE 0.204 0.044 S 0.193 0.322 / 461 19222 SENSE 0.255 0.072 T 0.622 0.034 S 473 19077 SENSE −0.049 0.669 / 0.2 0.227 / 474 19178 SENSE 0.303 0 S 0.592 0.001 S 477 70809 SENSE 0.128 0.093 T 0.224 0.185 T For other responses: S: represents the transgenic plants showed statistically significant trait improvement as compared to the reference (p < 0.05) T: represents the transgenic plants showed a trend of trait improvement as compared to the reference, preferably with p < 0.2 /: represents the transgenic plants didn't show any alteration or had unfavorable change in traits examined compared to the reference in the current dataset

J. Late Plant Growth and Development Screen

This example sets forth a soil based phenotypic platform to identify genes that confer advantages in the processes of leaf development, flowering production and seed maturity to plants.

Arabidopsis plants were grown on a commercial potting mixture (Metro Mix 360, Scotts Co., Marysville, Ohio) consisting of 30-40% medium grade horticultural vermiculite, 35-55% sphagnum peat moss, 10-20% processed bark ash, 1-15% pine bark and a starter nutrient charge. Soil was supplemented with Osmocote time-release fertilizer at a rate of 30 mg/ft³. T2 seeds were imbibed in 1% agarose solution for 3 days at 4° C. and then sown at a density of ˜5 per 2½″ pot. Thirty-two pots were ordered in a 4 by 8 grid in standard greenhouse flat. Plants were grown in environmentally controlled rooms under a 16 h day length with an average light intensity of −200 μmoles/m²/s. Day and night temperature set points were 22° C. and 20° C., respectively. Humidity was maintained at 65%. Plants were watered by sub-irrigation every two days on average until mid-flowering, at which point the plants were watered daily until flowering was complete.

Application of the herbicide glufosinate was performed to select T2 individuals containing the target transgene. A single application of glufosinate was applied when the first true leaves were visible. Each pot was thinned to leave a single glufosinate-resistant seedling ˜3 days after the selection was applied.

The rosette radius was measured at day 25. The silique length was measured at day 40. The plant parts were harvested at day 49 for dry weight measurements if flowering production was stopped. Otherwise, the dry weights of rosette and silique were carried out at day 53. The seeds were harvested at day 58. All measurements were analyzed as quantitative responses according to example 1M.

TABLE 12 a list of recombinant nucleotides that improve late plant growth and development Pep Rosette Dry Weight Rosette Radius Seed Dry Weight Silique Dry Weight Silique Length SEQ con- p- p- p- p- p- ID struct_id delta value c delta value c delta value c delta value c delta value c 289 19915 0.234 0.027 S 0.2 0.002 S 0.214 0.142 T 0.165 0.138 T −0.172 0.863 / 373 72772 0.194 0.291 / 0.022 0.068 T 0.259 0.003 S 0.102 0.343 / −0.223 0.889 / 403 13958 −0.065 0.797 / −0.279 0.863 / 0.146 0.041 S 0.092 0.177 T 0.009 0.158 T 405 10483 −0.073 0.946 / 0.302 0.002 S 0.288 0.022 T 0.592 0 S 0.137 0 S 412 12904 0.048 0.131 T 0.149 0.003 S 0.349 0.002 S 0.061 0.066 T −0.045 0.961 / 419 15142 −0.211 0.945 / 0.074 0.076 T 0.284 0.002 S −0.088 0.984 / 0.014 0.374 / 424 13005 −0.175 0.954 / 0.091 0.014 S 0.629 0.013 S 0.169 0.106 T −0.031 0.627 / 425 10203 0.2 0.036 S −0.023 0.587 / −0.757 0.922 / −0.059 0.756 / 0.018 0.15 T 426 11327 −0.046 0.747 / 0.056 0.138 T 0.327 0.08 T −0.109 0.94 / 0.009 0.142 T 427 11814 −0.127 0.799 / −0.085 0.866 / 0.397 0.016 S −0.184 0.91 / 0.05 0.236 / 428 13003 0.004 0.47 / −0.018 0.589 / 0.78 0.003 S −0.168 0.939 / −0.264 0.94 / 429 13949 −0.009 0.538 / −0.309 0.953 / 0.719 0.008 S −0.214 0.995 / 0.002 0.476 / 430 16416 0.396 0.001 S 0.099 0.03 S −0.654 0.999 / 0.034 0.187 T 0.013 0.13 T 431 16438 −0.501 0.802 / −0.516 0.9 / 0.63 0.021 S −0.968 0.842 / −0.461 0.905 / 432 17124 −0.226 0.898 / −0.022 0.618 / 0.702 0.012 S −0.479 0.942 / −0.055 0.99 / 433 19132 0.149 0.133 T 0 0.5 / −0.229 0.965 / 0.198 0.019 S −0.232 0.974 / 434 17922 0.206 0.012 S −0.002 0.52 / 0.541 0.037 S −0.017 0.757 / 0.028 0.3 / 435 19719 0.301 0.016 S 0.074 0.178 T −0.395 0.988 / 0.112 0.246 / −0.031 0.608 / 436 14274 0.03 0.411 / 0.131 0.087 T 0.429 0.009 S −0.086 0.948 / −0.181 0.968 / 436 17336 0.425 0.021 S −0.129 0.934 / −0.343 0.949 / 0.09 0.143 T 0.018 0.443 / 437 17735 −0.377 0.995 / −0.194 0.977 / 0.663 0.024 S −0.315 1 / −0.024 0.648 / 438 19249 −0.284 0.977 / −0.166 0.768 / 0.337 0.046 S −0.101 0.796 / 0.053 0.076 T 439 18513 0.194 0.202 / 0.096 0.112 T 0.248 0.159 T −0.13 0.676 / −0.072 0.802 / 440 11517 −0.033 0.586 / 0.073 0.052 T 0.133 0.25 / 0.145 0.217 / −0.016 0.762 / 441 12363 0.204 0.135 T −0.087 0.926 / 0.578 0.013 S 0.188 0.053 T 0.036 0.176 T 442 12922 0.202 0.003 S −0.035 0.928 / 0.453 0.14 T 0.164 0.096 T 0.006 0.298 / 443 15360 0.36 0.018 S −0.046 0.728 / −0.141 0.75 / 0.07 0.05 T 0.049 0.099 T 444 16028 0.341 0.032 S −0.036 0.548 / 0.044 0.403 / 0.18 0.034 S −0.015 0.604 / 445 16648 −0.49 0.989 / 0.033 0.374 / 0.471 0.025 S −0.169 0.8 / 0.018 0.228 / 446 16705 0.227 0.072 T −0.168 0.985 / 0.502 0.001 S −0.228 0.996 / −0.045 0.932 / 447 16715 0.011 0.442 / 0.059 0.161 T 0.485 0.042 S −0.087 0.724 / 0.058 0.03 S 448 17316 −0.047 0.812 / 0.047 0.08 T 0.109 0.391 / −0.172 0.747 / 0.229 0.008 S 449 17331 −0.451 0.979 / −0.156 0.916 / 0.443 0.001 S −0.11 0.761 / 0.043 0.069 T 450 17339 0.306 0.026 S 0.152 0.024 S −0.738 0.936 S 0.095 0.369 / 0.008 0.356 / 451 17420 −0.171 0.931 / −0.242 0.856 / 0.828 0.015 S −0.291 0.817 / −1.008 0.898 / 452 17446 −0.226 0.909 / −0.038 0.673 / 0.302 0.026 S 0.145 0.118 T −0.001 0.522 / 453 17487 −0.331 0.966 / 0.074 0.016 S 0.479 0.045 S −0.209 0.995 / 0.04 0.132 T 454 17740 −0.036 0.641 / 0.016 0.414 / 0.763 0.057 T 0.087 0.15 T 0.095 0 S 455 17752 0.35 0.041 S −0.107 0.673 / −0.619 0.915 / 0.343 0.004 S 0.022 0.294 / 456 18021 −0.252 0.947 / −0.131 0.836 / 0.287 0.079 T −0.249 0.885 / −0.018 0.64 / 457 18245 −0.227 0.99 / −0.031 0.629 / 0.422 0.011 S −0.126 0.758 / −0.048 0.827 / 458 18617 −0.193 0.955 / −0.3 0.95 / 0.877 0.001 S −0.328 0.971 / 0.075 0.077 T 459 18734 0.248 0.043 S 0.033 0.192 T −0.959 0.981 / 0.059 0.146 T −0.012 0.618 / 460 18823 0.229 0.114 T 0.069 0.181 T −0.056 0.677 / 0.282 0.048 S 0.032 0.24 / 461 19222 0.591 0.014 S 0.045 0.304 / −0.258 0.767 / 0.156 0.1 T −0.076 0.698 / 462 19430 0.362 0.024 S −0.02 0.776 / −0.751 0.857 / 0.036 0.281 / −0.231 0.848 / S: represents the transgenic plants showed statistically significant trait improvement as compared to the reference (p < 0.05) T: represents the transgenic plants showed a trend of trait improvement compared to the reference, preferably with p < 0.2 /: represents the transgenic plants didn't show any alteration or had unfavorable change in traits examined compared to the reference in the current dataset

K. Low Nitrogen Tolerance Screen

Under low nitrogen conditions, Arabidopsis seedlings become chlorotic and have less biomass. This example sets forth the low nitrogen tolerance screen to identify Arabidopsis plants transformed with the gene of interest that are altered in their ability to accumulate biomass and/or retain chlorophyll under low nitrogen condition.

T2 seeds were plated on plates containing 0.5×N-Free Hoagland's T 0.1 mM NH₄NO₃ T 0.1% sucrose T 1% phytagel media and grown under standard light and temperature conditions. At 12 days of growth, plants were scored for seedling status (i.e., viable or non-viable) and root length. After 21 days of growth, plants were scored for visual color, seedling weight, number of green leaves, number of rosette leaves, root length and formation of flowering buds. A photograph of each plant was also taken at this time point.

The seedling weight and root length were analyzed as quantitative responses according to example 1M. The number green leaves, the number of rosette leaves and the flowerbud formation were analyzed as qualitative responses according to example 1L. We considered that the transgenic plants grew better under the low nitrogen condition evidenced by having more green leaves or greener leaves, compared to the reference. In addition, the change in the root length in either direction, i.e., either increase or decrease will benefit plant growth. Transgenic plants with increased root length under a low nitrogen condition will enable plants to obtain nutrient from a farther distance, whereas transgenic plants with decreased root length while maintain a healthy growth evidenced by green leaves may have developed an intrinsic mechanism of using nitrogen source efficiently.

TABLE 13 a list of recombinant nucleotides that improve low nitrogen availability tolerance in plants Number of flowerbud Number of rosette leavels Pep formation green leaves Root Length at day 21 Rosette Weight SEQ Con- RS p- RS p- p- RS p- p- ID struct_id mean value c mean value c delta value c mean value c delta value c 241 74518 −0.141 0.97 / −0.123 1 / 0.097 0.006 T −0.532 0.983 / 0.104 0.007 S 315 12627 −0.881 1 / 1.713 0.001 S −0.222 0.052 S 1.622 0.008 S −0.037 0.136 / 316 12813 −1.269 1 / 1.151 0.011 S −0.01 0.89 / 1.858 0.001 S 0.14 0 S 317 14945 −1.131 1 / 0.899 0.014 S −0.056 0.486 / 0.305 0.289 / −0.038 0.587 / 318 15345 −0.158 0.626 / 0.961 0.014 S −0.352 0.004 S −0.308 0.739 / 0.069 0.297 / 319 15348 −0.582 0.937 / 0.755 0.015 S −0.17 0.082 T 0.923 0.046 S −0.033 0.214 / 320 16325 −0.947 0.999 / 0.995 0.003 S −0.204 0.079 T 1.15 0.01 S −0.014 0.652 / 321 16702 −0.315 0.997 / 0.567 0.023 S 0.16 0.01 S 0.572 0.071 T 0.012 0.614 / 322 16836 −1.291 1 / 0.149 0.098 T 0.141 0.029 S 2.117 0 S 0.035 0.247 / 323 17002 −1.153 1 / 0.32 0.013 S 0.209 0.007 S 1.818 0.001 S 0.131 0 S 324 17012 −1.201 1 / 0.348 0.025 S 0.291 0.002 S 1.485 0.001 S 0.082 0.107 T 325 17017 −0.352 1 / 0.982 0.003 S −0.112 0.159 T 0.276 0.127 T −0.009 0.725 / 326 17344 −1.897 1 / 0.736 0.039 S 0.111 0.181 T 1.344 0.02 S 0.076 0.001 S 327 17426 −1.364 1 / 1.185 0.002 S −0.218 0.008 S 0.814 0.094 T −0.076 0.034 / 328 17655 −1.059 1 / 1.094 0.002 S −0.084 0.208 / 1.656 0 S 0.024 0.637 / 329 17656 −1.309 1 / 0.465 0.04 S 0.107 0.228 / 1.317 0.001 S −0.046 0.058 / 330 17906 −1.21 1 / 0.058 0.369 / 0.213 0 S 1.251 0.006 S 0.057 0.262 / 331 18278 0.025 0.45 / 0.838 0.003 S 0.04 0.592 / 2.056 0.001 S 0.016 0.667 / 332 18822 −0.47 1 / 0.697 0 S 0.189 0.029 S 1.17 0.001 S 0.048 0.07 T 333 18881 1.062 0.022 S −0.365 0.949 / 0.08 0.211 / −1.211 1 / 0.006 0.845 / 334 19213 −0.095 0.712 / −0.298 1 / 0.18 0.001 S −0.802 1 / 0.056 0.062 T 335 19239 −0.187 0.931 / 1.466 0 S −0.104 0.186 T 1.297 0.006 S −0.048 0.187 / 336 19247 −0.346 0.913 / 0.274 0.022 S 0.013 0.833 / 1.818 0.001 S 0.088 0.216 / 337 19460 −0.526 0.994 / 1.427 0 S −0.004 0.932 / 0.952 0.01 S 0.003 0.952 / 338 19512 −0.546 1 / 1.611 0 S 0.152 0.011 S 0.824 0.001 S 0.041 0.226 / 339 19533 −0.283 0.929 / 1.909 0 S 0.072 0.353 / 1.904 0.001 S −0.002 0.952 / 340 19603 −0.25 0.932 / 0.287 0.213 / 0.208 0.005 S 0.234 0.214 / 0.135 0.021 S 341 72126 0.337 0.017 S −0.447 0.944 / −0.149 0.059 T 0.23 0.147 T 0.253 0 S 342 72437 0.907 0.016 S −0.36 0.989 / 0.111 0.049 S −0.689 0.999 / 0.09 0.005 S 343 72441 0.354 0.011 S 0.57 0.002 S −0.115 0.078 T 0.269 0.124 T −0.041 0.361 / 344 72639 0.578 0.065 T −0.198 0.956 / 0.23 0.001 S −0.181 0.756 / 0.13 0.005 S 364 19058 1.236 0.008 S −0.087 0.974 / −0.103 0.244 / −0.326 0.94 / 0.123 0.066 T 370 16403 −0.972 1 / 0.63 0.023 S −0.182 0.006 S 1.751 0.002 S −0.028 0.202 / 371 17737 −1.124 1 / 0.352 0.038 S 0.059 0.512 / 1.404 0.017 S −0.038 0.381 / 372 18395 −0.567 1 / 0.522 0.023 S 0.182 0.004 S 0.935 0.007 S 0.027 0.318 / 373 72772 0.439 0.019 S −0.113 0.827 / 0.211 0.006 S −0.141 0.739 / 0.106 0.006 S 376 11409 0.001 0.498 / 0.327 0.094 T −0.069 0.316 / 0.264 0.287 / 0.008 0.843 / 438 19249 −0.834 1 / 0.257 0.058 T 0.061 0.25 / 1.01 0.004 S 0.038 0.438 / 478 72091 −0.803 1 / −0.273 1 / 0.526 0 S 1.033 0.029 S 0.167 0.003 S S: represents the transgenic plants showed statistically significant trait improvement as compared to the reference (p < 0.05) T: represents the transgenic plants showed a trend of trait improvement compared than the reference, preferably with p < 0.2 /: represents the transgenic plants didn't show any alteration or had unfavorable change in traits examined compared to the reference in the current dataset

L. Statistic Analysis for Qualitative Responses

TABLE 14 a list of responses analyzed as qualitative responses response screen categories (success vs. failure) wilting response risk drought tolerance screen non-wilted vs. wilted score growth stage at day 14 heat stress tolerance screen 50% of plants reach stage1.03 vs. not growth stage at day 14 salt stress tolerance screen 50% of plants reach stage1.03 vs. not growth stage at day 14 PEG induced osmotic stress 50% of plants reach stage1.03 vs. not tolerance screen growth stage at day 7 cold germination stress tolerance 50% of plants reach stage 0.5 vs. not screen number of rosette leaves shade tolerance-low light screen 5 leaves appeared vs. not at day 23 flower bud formation at Shade tolerance-low light screen flower buds appear vs. not day 23 leaf angle at day 23 Shade tolerance-low light screen >60 degree vs. <60 degree number of green leaves at low nitrogen tolerance screen 6 or 7 leaves appeared vs. not day 21 number of rosette leaves low nitrogen tolerance screen 6 or 7 leaves appeared vs. not at day 21 Flower bud formation at low nitrogen tolerance screen flower buds appear vs. not day 21

Plants were grouped into transgenic and reference groups and were scored as success or failure according to Table 14. First, the risk (R) was calculated, which is the proportion of plants that were scored as of failure plants within the group. Then the relative risk (RR) was calculated as the ratio of R (transgenic) to R (reference). Risk score (RS) was calculated as −log₂ ^(RR). Subsequently the risk scores from multiple events for each transgene of interest were evaluated for statistical significance by t-test using S-PLUS statistical software (S-PLUS 6, Guide to statistics, Insightful, Seattle, Wash., USA). RS with a value greater than 0 indicates that the transgenic plants perform better than the reference. RS with a value less than 0 indicates that the transgenic plants perform worse than the reference. The RS with a value equal to 0 indicates that the performance of the transgenic plants and the reference don't show any difference.

M. Statistic Analysis for Quantitative Responses

TABLE 15 a list of responses analyzed as quantitative responses response screen seed yield drought stress tolerance screen seedling weight at day 14 heat stress tolerance screen root length at day 14 heat stress tolerance screen seedling weight at day 14 salt stress tolerance screen root length at day 14 salt stress tolerance screen root length at day 11 salt stress tolerance screen seedling weight at day 14 PEG induced osmotic stress tolerance screen root length at day 11 PEG induced osmotic stress tolerance screen root length at day 14 PEG induced osmotic stress tolerance screen rosette area at day 8 cold shock tolerance screen rosette area at day28 cold shock tolerance screen difference in rosette area cold shock tolerance screen from day 8 to day 28 root length at day 28 cold stress tolerance screen seedling weight at day 23 Shade tolerance-low light screen petiole length at day 23 Shade tolerance-low light screen root length at day 14 Early plant growth and development screen seedling weight at day14 Early plant growth and development screen rosette radius at day 25 Late plant growth and development screen seed dry weight at day 58 Late plant growth and development screen silique dry weight at day 53 Late plant growth and development screen silique length at day 40 Late plant growth and development screen Seedling weight at day 21 Low nitrogen tolerance screen Root length at day 21 Low nitrogen tolerance screen The measurements (M) of each plant were transformed by log₂ calculation. The Delta was calculated as log₂M(transgenic)−log₂M(reference). Subsequently the mean delta from multiple events of the transgene of interest was evaluated for statistical significance by t-test using S-PLUS statistical software (S-PLUS 6, Guide to statistics, Insightful, Seattle, Wash., USA). The Delta with a value greater than 0 indicates that the transgenic plants perform better than the reference. The Delta with a value less than 0 indicates that the transgenic plants perform worse than the reference. The Delta with a value equal to 0 indicates that the performance of the transgenic plants and the reference don't show any difference.

Example 2 Identification of Homologs

A BLAST searchable “All Protein Database” was constructed of known protein sequences using a proprietary sequence database and the National Center for Biotechnology Information (NCBI) non-redundant amino acid database (nr.aa). For each organism from which a DNA sequence provided herein was obtained, an “Organism Protein Database” was constructed of known protein sequences of the organism; the Organism Protein Database is a subset of the All Protein Database based on the NCBI taxonomy ID for the organism.

The All Protein Database was queried using amino acid sequence of cognate protein for gene DNA used in trait-improving recombinant DNA, i.e., sequences of SEQ ID NO: 240 through SEQ ID NO: 478 using “blastp” with E-value cutoff of 1e-8. Up to 1000 top hits were kept, and separated by organism names. For each organism other than that of the query sequence, a list was kept for hits from the query organism itself with a more significant E-value than the best hit of the organism. The list contains likely duplicated genes, and is referred to as the Core List. Another list was kept for all the hits from each organism, sorted by E-value, and referred to as the Hit List.

The Organism Protein Database was queried using amino acid sequences of SEQ ID NO: 240 through SEQ ID NO: 478 using “blastp” with E-value cutoff of 1e-4. Up to 1000 top hits were kept. A BLAST searchable database was constructed based on these hits, and is referred to as “SubDB”. SubDB was queried with each sequence in the Hit List using “blastp” with E-value cutoff of 1e-8. The hit with the best E-value was compared with the Core List from the corresponding organism. The hit is deemed a likely ortholog if it belongs to the Core List, otherwise it is deemed not a likely ortholog and there is no further search of sequences in the Hit List for the same organism. Likely orthologs from a large number of distinct organisms were identified and are reported by amino acid sequences of SEQ ID NO: 479 to SEQ ID NO: 12463. These orthologs are reported in Tables 2 as homologs to the proteins cognate to genes used in trait-improving recombinant DNA.

Example 3 Consensus Sequence Build

ClustalW program was selected for multiple sequence alignments of the amino acid sequence of SEQ ID NO:439 and 25 homologs. Three major factors affecting the sequence alignments dramatically are (1) protein weight matrices; (2) gap open penalty; (3) gap extension penalty. Protein weight matrices available for ClustalW program include Blosum, Pam and Gonnet series. Those parameters with gap open penalty and gap extension penalty were extensively tested. On the basis of the test results, Blosum weight matrix, gap open penalty of 10 and gap extension penalty of 1 were chosen for multiple sequence alignment. Attached are the sequences of SEQ ID NO: 439, its homologs and the consensus sequence at the end. The symbols for consensus sequence are (1) uppercase letters for 100% identity in all positions of multiple sequence alignment output; (2) lowercase letters for >=70% identity; symbol; (3) “X” indicated <70% identity; (4) dashes “-” meaning that gaps were in >=70% sequences.

SEQ ID NO : 5211 :------------------------------------------------------------ 12100 :------------------------------------------------------------ 6033 :------------------------------------------------------------ 5630 :------------------------------------------------------------ 2801 :------------------------------------------------------------ 11474 :------------------------------------------------------------ 12365 :------------------------------------------------------------ 9090 :------------------------------------------------------------ 439 :------------------------------------------------------------ 11419 :------------------------------------------------------------ 11201 :------------------------------------------------------------ 4683 :------------------------------------------------------------ 1624 :------------------------------------------------------------ 11490 :------------------------------------------------------------ 9137 :------------------------------------------------------------ 10769 :MIGTRVLAHSRVDPAIRWGVAARGRVVFAAIRWGAAARGRVVFAAVRWGAAARGTKREAG 2036 :------------------------------------------------------------ 1472 :------------------------------------------------------------ 2526 :------------------------------------------------------------ 12153 :------------------------------------------------------------ 2333 :------------------------------------------------------------ 8918 :------------------------------------------------------------ 12149 :------------------------------------------------------------ 6330 :------------------------------------------------------------ 11407 :------------------------------------------------------------ 9050 :------------------------------------------------------------ consensus :------------------------------------------------------------ 12464 -------------------MSCFACCGDEDTQ-VPDTRAQYPGHHPAR------------ -------------------MSCFACCGDEDTQ-VPDTRAQYPGHHPAR------------ -------------------MSCFACCGDEDTQ-VPDTRAQYPGHHPAR------------ -------------------MSCFACCGDEDTQ-VPDTRTQYPGHHPAR------------ -------------------MSCFACCGDEDTQGVPDNRNPYPGNHPAR------------ -------------------MSCLACCGGEDTQRTPDNGGPYPGGYPPR------------ -------------------MSCLACCGGEDTQRTPDNGGPYPGGYPPR------------ -------------------MSCFVCCGDEDTQRAPDNRNQYXKAIQQG------------ -------------------MSCFGCCGEDDDMHKTADYGGRHNQAKHFPPG--------- -------------------MSCFSCCDDDDMHRATDNGPFMAHNSAGN------------ -------------------MSCFSCCDDDDMHRATDNGPFMAHNSAGN------------ -------------------MGCFSCCGADDVGKKKKRDDPYVPIPDPG--G--------- -------------------MGFLCCSGKPSKRLESSSINENNSNIKRKDQTHVTSGSLKM -------------------MGFLCFSGKSSKRSENSSIDENNSNIKRKDQTQLTSGSMKV -------------------MGWIPCSGKSSGKTKKRSDSDENLSRNCSVSASERS----- QETSTSETKKTKRKWGRGFCGMASHEVEEPLTSETKKTKRKWGRGFCGMASHEAEEPLTS ------------------MKILLGVGINGGLFGSCVSSRSKVDSSTSGISSHFEIKSTN- ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ----------------------MAAADTSRVFLILIIALVMVIVVLLGICWRFLGPGIMR -------------------xxxxxxxxxxxxxxxxxxxxxxxxxxxxx--x--------- ------------------ADAYRPSDQPPKGPQPVKMQPIAVPAIPVDEIREVTKGFGDE ------------------ADAYRPSDQPPKGPQPVKMQPIAVPAIPVDEIREVTKGFGDE ------------------ADAYRPSDQPPKGPQPVKMQPIAVPAIPVDEIREVTKGFGDE ------------------ADAYRPADQPPKGSQPVKMQPIAVPAIPVDELREVTKGFGDE ------------------SDAYRTADPTPRGPQPVKVQPIAVPIIPVDEIREVTKNFGDE ------------------DDAYRTADPTPRGAQPLKMQPITVPTIPVEEIREVTVAFGDE ------------------DDAYRTADPTPRGAQPLKMQPITVPTIPVEEIREVTVAFGDE ------------------NDAYRTADPTPKGPQPVKVQPIAVPTIPMDEIREKNCTGGDE ----------------NDARHHQASETAQKGPPVVKLQPIEVPIIPFSELKEATDDFGSN ------------------NGGQRATESAQRETQTVNIQPIAVPSIAVDELKDITDNFGSK ------------------NGGQRATESAQRETQTVNIQPIAVPSIAVDELKDITDNFGSK ----------------NYGRSKPGPPAPSRSPPTSRNLPIAVPAIPLDEIKGITKNFSSD KPYVNNLSKEGESKDDQLSLDVKSLNMKDEISKDRRSNGKQAQTFTFEELAAATSNFRSD KPYVNDSREEGASKDDQLSLDVKSLNLKDEISKDIRNNGNPAQTFTFEELVAATDNFRSD -----------------------KAKSSVSESRSRGSDNIVAQTFTFSELATATRNFRKE ETKKKRKNVAASSEPDKKRWFKNKIWKKKKAKNEQLATLVKEISLATKLNSAMHVNINLS -----------NVSKDQPTTSNSEHNLPTLTPEDELKVASRLRKFGFNDLKMATRNFRPE ----------------MGSKYSKATNSINDALNSSYLVPFESYRFPLVDLEEATNNFD-- ----------------MGSKYSKATNSINDALSSSYLVPFESYRVPLVDLEEATNNFDDK ----------------MGSKYSKATNSISDASNSRYGVPFENYRVPLVDLEEATNNFDDN ----------------MGSKYSKATNSINDASNSSYRVPFESLRVPFVDLQEATNNFDDK -------------------------------LNSSYRVPFESFRVPFVDLQEATNNFDEK -------------------------------LNSSYRVPFESFRVPFVDLQEATNNFDEK -------------------------------LNSSYRVPFESFRVPFVDLQEATNNFDEK ------------------MRSKDSKETTYISDTTSYRFPVESSQIPFAALQEATNNFNCN ---------------RLLRPRRCPSEVPEYFSGNMSGNLRTITYFDYVTLKKATKDFHQK ----------------xxxxxxxxxxxxxxxxxxxxxxpxxxxxxxxxxxxxxtxxfxxx ALIGEGSFGRVYLGVLRNG----------RSAAVKKLDS-NKQPDQEFLA-QVSMVSRLK ALIGEGSFGRVYLGVLRNGX---------GVAAVKKLDS-NKQPDQEFLSXQVSMVSRLK ALIGEGSFGRVYLGVLRNG----------RSAAVKKLDS-NKQPDQEFLA-QVSMVSRLK ALIGEGSFGRVYLGVLRNGR---------SAXRVKKLDS-NKQPDQEFLXAQVSMVSRLK ALIGEGSFGRVYFGVLRNG----------RSAAVKKLDS-SKQPDQEFLA-QVSMVSRLK ALIGEGSFGRVYFGVLKNG----------RSAAIKKLDS-SKQPEQEFLA-QVSMVSRLK ALIGEGSFGRVYFGVLKNG----------RSAAIKKLDS-SKQPEQEFLA-QVSMVSRLK ALIGEGSFGRVYFGTLRNG----------RGAAIKKLDS-SKQPDQELLA-QVSMVSRLK SLIGEGSYGRVYYGVLNND----------LPSAIKKLDS-NKQPDNEFLA-QVSMVSRLK ALIGEGSYGRVYHGVLKSG----------RAAAIKKLDS-SKQPDREFLA-QVSMVSRLK ALIGEGSYGRVYHGVLKSG----------RAAAIKKLDS-SKQPDREFLA-QVSMVSRLK ALIGEGSYARVFFGVLRDG----------RRSAVKKLDS-SKQPDQEFLV-QVSAVSRLK CFLGEGGFGKVYKGYLDK---------INQAVAIKQLDR-NGVQGIREFVVEVVTLSLAD CFLGEGGFGKVYKGYLEK---------INQVVAIKQLDQ-NGLQGIREFVVEVLTLSLAD CLIGEGGFGRVYKGYLAS---------TGQTAAIKQLDH-NGLQGNREFLVEVLMLSLLH MNICPTQTYEEHSGTYLR---------NLAVIAVKQLDK-DGLQGNREFLVEVLMLSLLH SLLGEGGFGCVFKGWIEENGTAPVKPGTGLTVAVKTLNH-DGLQGHKEWLAEVNFLGDLG ---GKGGFGKVYRGVLRDG----------TKVALKRHNR-DSGQSIEPFRTEIEILSRRS FFIGAGVFGKVYKGVLRDG----------TKVALKRRKP-ESSQGIEEFETEIEILSFCS FFIAEGGFGKVYRGVLRDG----------TKVALKRHNC-DSQQSIEEFRTEIEILSRRS FLIGWGVFGKVYMGVLRNG----------TKVALKKHMP-ESSQGIEEFRTEIEILSLCS FHIGLGGFGKVYRGVLRDG----------TKVALKRCKR-ESSQGIEEFRTEIEILSFCS FHIGLGGFGKVYRGVLRDG----------TKVALKRCKR-ESSQGIEEFRTEIEILSFCS FHIGLGGFGKVYRGVLRDG----------TKVALKRCKR-ESSQGIEEFQTEIEILSFCS SLIGLGGFGTVYRGVLCDG----------TKVALKRCKL-ESSQGIEEFQTEIEMLSHFR NQLGRGGFGPVYLGKLDDG----------RKVAVKQLSVGKSGQGESEFFMEVNMITSIQ xxigxgxfgxvyxGvlxxg----------xxxaxKxxxx-xxxxxxexxxxxxxxxsxxx HENVVELLGYCADGTLRVLAYEFATMGSLHDMLHGRKGVKG-AQPGPVLSWSQRVKIAVG HENXVELLGYCXDGTLRVLAYEFATMGSLHDMLHGRKGVKG-AQPGPVLXWSQRXKIAVG HENVVELLGYCADGTLRVLAYEFATMGSLHDMLHGRKGVKG-AQPGPVLSWSQRVKIAVG HENVVELLGYCADGTLRVLAYEFATMGSLHDMLHGRKGVKG-AQPGPVLSWLQRVKIAVG HEHVVELLGYCVDGNLRVLAYEFATMGSLHDMLHGRKGVKG-AQPGPVLSWAQRVKIAVG HGNVVELLGYCVDGNTRILAYEFATMGSLHDMLHGRKGVKG-AQPGPVLSWTQRVKIAVG HGNVVELLGYCVDGNTRILAYEFATMGSLHDMLHGRKGVKG-AQPGPVLSWTQRVKIAVG HENVVELLGYCLDGNTRVLAYEFATMGSLHDMLHGRKGVKG-AQPGPVLSWIQRVKIAVG HDNFVQLLGYCVDGNSRILSYEFANNGSLHDILHGRKGVKG-AQPGPVLSWYQRVKIAVG DENVVELLGYCVDGGFRVLAYEYAPNGSLHDILHGRKGVKG-AQPGPVLSWAQRVKIAVG DENVVELLGYCVDGGFRVLAYEYAPNGSLHDILHGRKGVKG-AQPGPVLSWAQRVKIAVG HENIIQLIGYCAGGSIRVLAYEYAPRGSLHDILHGKKGVKG-AQPGPALSWMQRVKIALS HPNLVKLIGFCAEGDQRLLVYEYMPLGSLENHLHDIP------PNRQPLDWNTRMKIAAG NPNLVKLIGFCAEGDQRLLVYEYMPLGSLENHLHDIP------PNRQPLDWNARMKIAAG HPNLVNLIGYCADGDQRLLVYEYMPLGSLEDHLHDIS------PSKQPLDWNTRMKIAAG HPNLVTLLGYCTECDQKILVYEYMPLGSLQDHLLDLT------PKSQPLSWHTRMKIAVD NPNLVKLIGYCIEDDQRLLVYEFLPRGSLENHLFRR---------SLPLPWSIRMKIALG HPHLVSLIGFCDERNEMILIYDYMENGNLKSHLYG--------SDLPTMSWEQRLEICIG HPHLVSLIGFCDERNEMILIYKYMENGNLKSHLYG--------SDLPSMSWEQRLEICIG HPHLVSLIGYCDGRNEMILIYDYMENGNLKSHLYG--------SDLPSMSWEQRLEICIG HPHLVSLIGYCDERNEMILIYEYMENGNLRSHLYG--------SDLPAMSWEQRLEICIG HPHLVSLIGYCDETNEMILVYDYIENGNLRSHLYG--------PDLPTMSWEQRLEICIG HPHLVSLIGYCDETNVMILVYDYIENGNLRSHLYG--------PDLPTMSWEQGLEICIG HPHLVSLIGYCDERNEMILVYDYIENGNLRSHLYG--------SDLPSMSWEQRLEICIG HPYLVSLIGYCDENNVTILIFKYMENGSLSSHLYG--------SYLPTMTWEQRLEICIG HKNLVRLVGCCSEGTERLLVYEYMKNKSLDKILFAAADAPAPASAPPFLNWRTRHQIIIG hxxxvxLxGyCxxxxxxxLxyexxxxgsLxxxLxgxxxxxx-xxxxpxxsWxqrxxIxxg AAKGLEYLHEKAQPHIIHRDIKSSNVLLFDDDVAKIADFDLSNQ-APDMAARLHSTRVLG AAKGLEYLHEKAQPHIIHRDIKSSNVLSFDDDVAKIADFDLSNQXAPDMAARLHSTRVLG AAKGLEYLHEKAQPHIIHRDIKSSNVLLFDDDVAKIADFDLSNQ-APDMAARLHSTRVLG AAKGLEYLHEKAQPHIMHRDIKSSNVLLFDDDVAKIADFDLSNQ-APDMAARLHSTRVLG AAKGLEYLHEKAQPHIIHRDIKSSNVLLFDDDVAKIADFDLSNQ-APDMAARLHSTRVLG AAKGLEYLHEKAQPHIIHRDIKSSNVLLFDDDVSKIADFDLSNQ-APDMAARLHSTRVLG AAKGLEYLHEKAQPHIIHRDIKSSNVLLFDDDVSKIADFDLSNQ-APDMAARLHSTRVLG AAKGLEYLHEKAQPHVIHRDIKSSNVLLFDDDVAKIADFDLSNQ-APDMAARLHSTRVLG AARGLEYLHEKANPHIIHRDIKSSNVLLFEDDVAKIADFDLSNQ-APDMAARLHSTRVLG AAKGLEYLHEKAQPHIIHRDIKSSNILLFDDDVAKIADFDLSNQ-APDMAARLHSTRVLG AAKGLEYLHEKAQPHIIHRDIKSSNILLFDDDVAKIADFDLSNQ-APDMAARLHSTRVLG AAKGLEFLHEKAEPRVVHRDIKSSNIMLFDNDVAKVGDFDVSNQ-SPDMAARLHSTRVLG AAKGLEYLHNEMKPPVIYRDLKCSNILLGEGYHPKLSDFGLAKV-GPSGDKTHVSTRVMG AAKGLEYLHNEMAPPVIYRDLKCSNILLGEGYHPKLSDFGLAKV-GPSGDHTHVSTRVMG AAKGLEYLHDKTMPPVIYRDLKCSNILLGDDYFPKLSDFGLAKL-GPVGDKSHVSTRVMG AARGLEYLHEVANPPVVYRDLKASNILLDGNFSAKLADFGLAKL-GPVGDKTHVTTRVMG AAKGLAFLHEEAKRPVIYRDFKTSNILLDAEYNAKLSDFGLAKD-GPEGDKTHISTRVMG AARGLHYLHTS---AVIHRDVKSTNILLDENFVAKITDFGISKK-GTELDQTHVSTDVKG AARGLYYLHTR---AVIHRDVKSINILLDENFVPKITDFGISKK-GTELDQTHLSTVVQG AARGLHYLHTN---GVMHRDVKSSNILLDENFVPKITDFGLSKT-RPQLYQTHVSTDVKG AARGLHYLHTS---AVIHRDVKSINILLDDNFVPKITDFGLSKT-GTELDQTHVSTAVKG AARGLHYLHTS---AVIHRDVKSINILLDENFVAKITDFGISKK-GTELDQTHLSTLVQG AARGLHYLHTS---AVIHRDVKSINILLDENFVAKITDFGISKK-GTELDQTHLSTLVQG AARGLHYLHTS---AVIHRDVKSINMLLDENFVAKITDFGLSKK-GTELDQTHLSTLVQG AARGLYYLHKN---AVIHRDVKSANILLDENFVAKTTDFGVSKT-RTELDQTHVSTVVKG IGRGLQYLHEESNLRIVHRDIKASNILLDDKFQPKISDFGLAR--FFPEDQTYLSTAFAG aaxGLxyLHxxxxxxxihRDxKssNxllxxxxvxKixDFxlsxx-xxxxxxxxxsTxvxG TFGYHAPEYAMTGQLSSKSDVYSFGVVLLELLTGRKPVDHTLPRGQQSLVTWATPRLSED TFGYHAPEYAMTGQLSSKSDVYSFGVVLLELLTGRKPVDHTLPRGQQSLVTWATPXLSED TFGYHAPEYAMTGQLSSKSDVYSFGVVLLELLTGRKPVDHTLPRGQQSLVTWATPRLSED TFGYHAPEYAMTGQLSSKSDVYSFGVVLLELLTGRKPVDHTLPRGQQSLVTWATPRLSED TFGYHAPEYAMTGQLSSKSDVYSFGVVLLELLTGRKPVDHTLPRGQQSLVTWATPRLSED TFGYHAPEYAMTGQLSSKSDVYSFGVVLLELLTGRKPVDHTLPRGQQSLVTWATPRLCED TFGYHAPEYAMTGQLSSKSDVYSFGVVLLELLTGRKPVDHTLPRGQQSLVTWATPRLCED TFGYHAPEYAMTGQLSSKSDVYSFGVVLLELLTGRKPVDHTLPRGQQSLVTWATPRLSED TFGYHAPEYAMTGQLNAKSDVYSFGVVLLELLTGRKPVDHRLPRGQQSLVTWATPKLSED TFGYHAPEYAMTGQLSSKSDVYSFGVVLLELLTGRKPVDHTLPRGQQSLVTWATPRLSED TFGYHAPEYAMTGQLSSKSDVYSFGVVLLELLTGRKPVDHTLPRGNR-VCYLGNARLSED TFGYHAPEYAMTGQLSTKSDVYSFGVVLLELLTGRKPVDHTLPRGQQSLVTWATPRLSED TYGYCAPDYAMTGQLTFKSDIYSFGVVLLELITGRKAIDQRKERGEQNLVAWARPMFKDR TYGYCAPDYAMTGQLTFKSDVYSFGVVLLELITGRKAIDQTKERSEQNLVAWARPMFKDR TYGYCAPEYAMTGQLTLKSDVYSFGVVLLEIITGRKAIDNSRCTGEQNLVAWARPLFKDR TYGYCAPEYAMSGKLTKMSDIYCFGVVLLELITGRRAIDTTKPTREQILVHWAAPLFKDK TYGYAAPEYVMTGHLSSKSDVYSFGVVLLEMLTGRRSMDKKRPNGEHNLVEWARPHLGER TFGYLDPEYFIKGRLTEKSDVYSFGVVLFEVLCARSAIVQSLPREMVNLAEWAVESHNNG TLGYLDPEYFIKGRLTEKSDVYSFGVVLFEVLCARSAIVQSLPREMVNLAEWAVESHNNG TFGYIDPEYFIKGRLTEKSDVYSFGVVLFEVLCARSAIVQSLPSEMVNLAEWAVESHNNG TVGYLDPEYFIRGQLTEKSDVYSFGVVLFEVLCARPAIAHSHSREMISLAEWAVESHNNG TIGYLDPEYFIRGQLTEKSDVYSFGVVLFEVLCARPAIVQSLPREMVNLAEWAVDSHNKG TIGYLDPEYFLRGQLTEKSDVYSFGVVLFEVLFARPAIVQSLPREMVSLAEWAVDSHNKG TIGYLDPEYFIRGQLTEKSDVYSFGVVLFEVLCARPAIVQSLPREMVNLAEWAVDSHNKG TLGYLDPEYVIRGKLTEKSDVYSFGVVLFKVLCARSAIVHYISKGLVTLAAWAMDSHKKG TLGYTAPEYAIRGELTVKADTYSFGVLVLEIISSRKNTDLNLPNEMQYLPEHAWRLYEQS TxGYxxPeYxxxGqLxxksDvYsFGVvlxexlxxRxxxxxxlprxxxxlxxwaxxxxxxx K-VRQCVDSRLGGD--YPPKAVAKFAAVAALCVQYEADFRPNMSIVVKALQPLLNAHAR- K-VRQCVDSRLGGD--YPPKAVAKFAAVAALCVQYEADFRPNMSIVVKALQPLLNAACAG K-VRQCVDSRLGGD--YPPKAVAKFAAVAALCVQYEADFRPNMSIVVKALQPLLNAHAR- K-VRQCVDSRLGGD--YPPKAVAKFAAVAALCVQYEADFRPNMSIVVKALQPLLNAHARA K-VRQCVDSRLGGD--YPPKAVAKFAAVAALCVQYEADFRPNMSIVVKALQPLLNARATN K-VRQCVDSRLGVE--YPPKSVAKFAAVAALCVQYEADFRPNMSIVVKALQPLLNARASN K-VRQCVDSRLGVE--YPPKSVAKFAAVAALCVQYEADFRPNMSIVVKALQPLLNARASN K-VRQCVDSRLGGD--YPPKAVAKFAAVAALCVQYEADFRPNMSIVVKALQPLLNARAAH K-VKQCVDARLGGD--YPPKAVAKLAAVAALCVQYEADFRPNMSIVVKALQPLLNARAVA K-VKQCVDARLNTD--YPPKAIAKMAAVAALCVQYEADFRPNMSIVVKALQPLLPRPVPS K-VKQCVDARLNTD--YPPKAIAKMAAVAALCVQYEADFRPNMSIVVKLFSLCCLDLYQV K-VKQCVDPRLEGD--YPPKAVAKMAAVAALCVQYEADFRPNMSIVVKALNPLLNSRPNN RNFSCMVDPLLQGQ--YPIRGLYQALAIAAMCVQEQPNMRPAVSDLVMALNYLASHKYDP RNFSGMVDPFLQGQ--YPIKGLYQALAIAAMCVQEQPNMRPAVSDVVLALNYLASHKYDP RKFSQMADPMIQGQ--YPPRGLYQALAVAAMCVQEQPNLRPVIADVVTALTYLASQRFDP KKFTKMADPLLDSK--YPLKGLYQALAISSMCLQEEAISRPLISDVVTALTFLADPNYDP RRFYRLIDPRLEGH--FSIKGAQKAAQLASRCLSRDPKARPLMSEVVDCLKPLPALKDMA Q-LEQIVDPNLADK--IRPESLRKFGDTAVKCLALSSEDRPSMGDVLWKLEYALRLQESV Q-LEQIIDPNLADK--ITPESLRKFGETAVKCLALSSEDRPSMGDVLWKLEYALRLQESV Q-LEQIIDPNLAAK--IRPESLRKFGETAVKCLALSSEDRPSMGDVLWKLEYALRLQESV Q-LEQIIAPNIAAK--IRPESLKKFGETVVKCLALSSEDRPSMGDVLWKLEYALRLQESV H-LEQIIDPDLAAK--IRPESLRKFGETAVKCLALSSEDRPSMGDVL------------- Q-LEQIVDPDLAAK--IRPESLRKFGETAVKCLALSSEDRPSMGDVL------------- Q-LEQIIDLNLAAK--IRPESLRKFGETAVKCLALSSGDRPSMGDVL------------- Q-LEQIVDPNLASK--IRPKYLNKFGETAVKCLADSGVDRPSVGDVL------------- K-ILELVDGRVQGGEGFEEKEVMLVCQIALLCVQPYPNSRPAMSEVVRMLTMKTDQSIPA x-xxqxxdxxlxxx--xxpxxxxkxxxxaxxCxxxxxxxRPxmxxvxxxlxxxxxxxxxx ATNPGEHAGS---------------------------------------------------- RPNPGEHAGS---------------------------------------------------- ATNPGEHAGS---------------------------------------------------- TNP----------------------------------------------------------- PGENAGS------------------------------------------------------- NPG----------------------------------------------------------- NPG----------------------------------------------------------- PGAEHAGR------------------------------------------------------ PGEGVII------------------------------------------------------- -------------------------------------------------------------- RHQACEFSPYPCLYVMK--------------------------------------------- RPASFTDAGERSGL------------------------------------------------ ---QVHSVQDSRRSPSRPGLDKDRGQ------------------------------------ ---QIHPFKDPRRRPSHPGLDKDNGRT----------------------------------- ---MSQPVQGSLFGPGTPPRSKRVV------------------------------------- ---PDDIEPLPISVPNYDKGISLREAEISLSGFEEKQVEDS--------------------- GPSYYLQTVQPERAGSSPDPNRTRVGSFSRNGSQHPRTLSIPNASPRHNQFLQDSPNPNGKQ I------------------------------------------------------------- I------------------------------------------------------------- I------------------------------------------------------------- I------------------------------------------------------------- -------------------------------------------------------------- -------------------------------------------------------------- -------------------------------------------------------------- -------------------------------------------------------------- PAKPAFLDRKNLNGDRDAASSDTATMEMMRSPAGYWMMTPSPMLEVDRPYDMSFGK------ xxxxxxxxxxxxxx------------------------------------------------

Example 4 Corn Transformation Construct

GATEWAY™ destination vectors (available from Invitrogen Life Technologies, Carlsbad, Calif.) were constructed for insertion of trait-improving DNA for corn transformation. The elements of each destination vector are summarized in Table 16 below and include a selectable marker transcription region and a DNA insertion transcription region. The selectable marker transcription region comprises a Cauliflower Mosaic Virus 35S promoter operably linked to a gene encoding neomycin phosphotransferase II (nptII) followed by both the 3′ region of the Agrobacterium tumefaciense nopaline synthase gene (nos) and the 3′ region of the potato proteinase inhibitor II (pinII) gene. The DNA insertion transcription region comprises a rice actin 1 promoter, a rice actin 1 exon 1 intron1 enhancer, an att-flanked insertion site and the 3′ region of the potato pinII gene. Following standard procedures provided by Invitrogen the att-flanked insertion region is replaced by recombination with trait-improving DNA, in a sense orientation for expression of a trait-improving protein and in a gene suppression orientation (i.e., either anti-sense orientation or in a sense- and anti-sense orientation) for a trait-improving suppression of a protein. Although the vector with trait-improving DNA inserted at the att-flanked insertion region is useful for plant transformation by direct DNA delivery, such as microprojectile bombardment, it is preferable to bombard target plant tissue with tandem transcription units that have been cut from the vector. For Agrobacterium-mediated transformation of plants the vector also comprises T-DNA borders from Agrobacterium flanking the transcription units. Vectors for Agrobacterium-mediated transformation are prepared with each of the trait-improving genes having a sequence of SEQ ID NO: 1 through SEQ ID NO: 151 and SEQ ID NO: 153 through SEQ ID NO: 239 with the DNA solely in sense orientation for expression of the cognate trait-improving protein and in a gene suppression orientation for suppression of the cognate protein. Each vector is transformed into corn callus which is propagated into a plant that is grown to produce transgenic seed. Progeny plants are self-pollinated to produce seed which is selected for homozygous seed. Homozygous seed is used for producing inbred plants, for introgressing the trait into elite lines, and for crossing to make hybrid seed. The progeny transgenic plants comprising the trait-improving DNA with a sequence of SEQ ID NO:1 through SEQ ID NO: 151 and SEQ ID NO: 153 through SEQ ID NO: 239 have one or more improved traits including, but not limited to increased yield and those disclosed in Table 3. Transgenic corn including inbred and hybrids are also produced with DNA from each of the identified homologs and provide seeds for plants with the improved trait of the cognate DNA of SEQ ID NO: 1 through SEQ ID NO: 151 and SEQ ID NO: 153 through SEQ ID NO: 239. Transgenic corn plants are also produced where the trait-improving DNA is transcribed by each of the promoters from the group selected from, a maize globulin 1 promoter, a maize oleosin promoter, a glutelin 1 promoter, an aldolase promoter, a zein Z27 promoter, a pyruvate orthophosphate dikinase (PPDK) promoter, a soybean 7S alpha promoter, a peroxiredoxin antioxidant (Per1) promoter and a CaMV 35S promoter.

Seed produced by the plants is provided to growers to enable production of corn crops with improved traits associated with the trait-improving DNA.

TABLE 16 Elements of an exemplary corn transformation vector FUNCTION ELEMENT REFERENCE DNA insertion Rice actin 1 promoter U.S. Pat. No. 5,641,876 transcription region Rice actin 1 exon 1, intron 1 U.S. Pat. No. 5,641,876 enhancer DNA insertion AttR1 GATEWAY ™Cloning Technology transcription region Instruction Manual (att-flanked insertin CmR gene GATEWAY ™Cloning Technology region) Instruction Manual ccdA, ccdB genes GATEWAY ™Cloning Technology Instruction Manual attR2 GATEWAY ™Cloning Technology Instruction Manual DNA insertion Potato pinII 3′ region An et al., (1989) Plant Cell 1: 115-122 transcription region selectable marker CaMV 35S promoter U.S. Pat. No. 5,858,742 transcription region nptII selectable marker U.S. Pat. No. 5,858,742 nos 3region U.S. Pat. No. 5,858,742 PinII 3′ region An et al., (1989) Plant Cell 1: 115-122 E. coli maintenance ColE1 origin of replication region F1 origin of replication Bla ampicillin resistance

Example 5 Soybean Transformation Construct

Constructs for use in transformation of soybean may be prepared by restriction enzyme based cloning into a common expression vector. Elements of an exemplary common expression vector are shown in Table 17 below and include a selectable marker expression cassette and a gene of interest expression cassette. The selectable marker expression cassette comprises Arabidopsis act 7 gene (AtAct7) promoter with intron and 5′UTR, the transit peptide of Arabidopsis EPSPS, the synthetic CP4 coding region with dicot preferred codon usage and a 3′ UTR of the nopaline synthase gene. The gene of interest expression cassette comprises a Cauliflower Mosaic Virus 35S promoter operably linked to a trait-improving gene in a sense orientation for expression of a trait-improving protein and in a gene suppression orientation (i.e., either anti-sense orientation or in a sense- and anti-sense orientation for a trait-improving suppression of a protein.

Vectors similar to that described above may be constructed for use in Agrobacterium mediated soybean transformation systems, with each of the trait-improving DNA having a sequence of SEQ ID NO: 1 though SEQ ID NO: 151 and SEQ ID NO: 153 through SEQ ID NO: 239 with the DNA solely in sense orientation for expression of the cognate protein and in a gene suppression orientation for suppression of the cognate protein. Transgenic soybean plants are produced comprising the trait-improving DNA with a sequence of SEQ ID NO: 1 through SEQ ID NO: 151 and SEQ ID NO: 153 through SEQ ID NO: 239 have one or more improved traits including, but not limited to, those disclosed in Table 3 and increased yield. Transgenic soybean plants are also produced with DNA from each of the identified homologs and provide seeds for plants with improved trait of the cognate DNA of SEQ ID NO: 1 through SEQ ID NO: 151 and SEQ ID NO: 153 through SEQ ID NO: 239. Transgenic soybean plants are also produced where the trait-improving DNA is transcribed by a desirable promoter including, but not limited to, the enhanced 35S promoter, napin promoter and Arabidopsis SSU promoter.

Seed produced by the plants is provided to growers to enable production of soybean crops with improved traits associated with the trait-improving DNA.

TABLE 17 Elements of an exemplary soybean transformation construct Function Element Reference Agro transformation B-ARGtu.right border Depicker, A. et al.,, (1982) Mol Appl Genet 1: 561-573 Antibiotic resistance CR-Ec.aadA-SPC/STR Repressor of primers from the ColE1 plasmid CR-Ec.rop Origin of replication OR-Ec.oriV-RK2 Agro transformation B-ARGtu.left border Barker, R. F. et al.,, (1983) Plant Mol Biol 2: 335-350 Plant selectable marker expression cassette Arabidopsis act 7 gene McDowell et al., (1996) Plant (AtAct7) promoter with Physiol. 111: 699-711. intron and 5′UTR 5′ UTR of Arabidopsis act 7 gene Intron in 5′UTR of AtAct7 Transit peptide region of Klee, H. J. et al.,, (1987) MGG Arabidopsis EPSPS 210: 437-442 Synthetic CP4 coding region with dicot preferred codon usage A 3′ UTR of the nopaline synthase U.S. Pat. No. 5,858,742 gene of Agrobacterium tumefaciens Ti plasmid Plant gene of interest expression cassette Promoter for 35S RNA from U.S. Pat. No. 5,322,938 CaMV containing a duplication of the −90 to −350 region Gene of interest insertion site Cotton E6 3′ end GenBank accession U30508

APPENDIX TABLE 3 SEQ ID NO: SEQ ID NOs of homologs 240: 7319 7772 4165 7279 8472 1915 241: 872 9283 6127 9719 4864 6242 8526 6419 7759 9073 2613 2268 4632 9988 706 4211 5868 5162 6778 2818 4446 8022 5640 2336 937 9010 7423 10353 8552 4128 4105 7686 12195 10669 12342 8692 5537 11579 2835 8650 5475 11890 7460 9427 2284 3244 11978 9829 4748 8553 1446 2403 7293 3548 12319 6834 10066 6183 4312 7543 5134 8322 2800 11545 6091 11097 3540 3961 7214 10438 1640 9780 4934 7927 2400 7549 12416 10157 1349 6290 7629 4403 10890 6442 2515 5801 12216 8987 5141 9726 6551 10160 5289 1354 4654 7838 11102 3968 2890 6186 628 8703 9371 3860 10153 8874 1345 7931 11204 11770 3018 3441 10577 10610 10499 8307 12271 1848 4425 1204 1537 11923 3133 4808 9940 6766 3234 12003 8649 7112 12207 10622 5119 3464 9955 6521 4120 9924 5693 8842 7406 4197 4325 11073 9174 6893 10059 1792 9442 8812 5665 9783 1361 6628 8108 6348 10795 6924 1868 12137 4042 2276 3365 6619 12076 2084 4511 3278 10300 4514 7688 1267 870 4951 2767 8580 11788 10100 7117 5046 6531 5445 9848 2178 713 10999 6411 646 5189 7310 10504 11929 1690 5343 6267 1010 5444 10776 7548 3144 4347 6416 9264 9668 1540 7457 1122 10665 8509 11546 9473 4244 3142 6550 4093 2863 10916 9567 862 7304 1912 11709 884 11773 4089 11785 2325 5602 8736 11430 3004 5891 11938 8737 6309 4091 10924 5306 970 8723 3683 9687 7150 3905 10712 8324 8543 6285 2682 5065 2993 8344 1928 12197 6661 3414 3878 8576 774 10904 8487 5985 7098 9655 5534 7770 12211 7227 6188 11837 8030 8147 9951 9758 683 5810 9658 7427 854 9096 9694 10883 8039 9649 1316 2610 8172 9902 11673 9763 499 2532 2273 1867 10674 11658 10467 11143 1561 1227 9980 2746 6047 9225 2913 6734 10827 3272 6723 9908 7466 1095 3459 6609 11165 9800 10526 4253 9446 9328 5243 6005 1744 3090 12421 3920 9832 3711 9011 8423 4461 6692 6831 8360 1571 3181 10685 9072 11904 1514 2794 8680 1183 2396 9496 723 3283 5147 998 10149 12448 9404 2278 9070 5576 1261 5939 3430 2638 11889 9203 5258 12274 5799 9522 2209 11401 4316 10154 7581 4238 1104 2565 2848 3349 4385 7993 4012 10842 544 2395 6432 11530 3630 6887 1938 8532 4631 7779 9935 6726 5294 3500 2088 5588 8751 10934 9077 12313 8073 6328 3806 12016 9891 2751 5347 3832 10482 524 4855 1451 4889 9957 9833 3328 3098 11887 579 2376 3260 1257 10421 5585 7953 6402 1187 8710 933 10081 11571 10018 11279 929 11738 10702 8395 1157 3651 6278 10269 5139 1814 9838 12108 7445 2303 9917 11909 2568 7488 10105 12154 11220 2690 3294 8852 2106 8583 3726 9139 4395 7992 7908 9159 5429 8677 5538 1997 10866 5592 7970 3940 8551 6443 4844 10921 7499 3865 12214 9624 9142 10614 3371 11020 5516 3879 2073 1240 10773 867 6888 483 7134 7633 4447 3518 9610 10005 4180 2410 2959 6221 10371 4837 6806 10032 9340 610 6464 3840 6788 8340 5255 11301 3620 11459 1054 9431 3644 6930 815 12034 4401 1154 10315 3519 4509 7105 5666 8850 3340 2021 10868 3167 2533 4785 3507 1879 1719 7972 9585 784 11284 10399 242: 6383 3426 9749 9579 6504 8571 11363 9729 2774 2824 6800 11836 10978 7535 243: 5229 2681 3233 1102 12450 7058 6882 3684 4692 2430 6687 2702 11159 493 3493 6575 9272 8970 4693 4714 7364 4741 11303 7436 6620 9708 652 2422 6738 8982 8262 3429 5618 10576 9432 10821 546 12282 7540 3060 4399 5507 4375 597 4290 6727 1992 2652 10629 2001 4620 7522 3946 5212 8061 3108 11936 9667 9717 244: 11270 10304 1123 8010 8141 2919 10052 3566 6143 245: 9076 1014 3740 10454 2125 974 3282 11533 12119 7082 8997 10377 246: 7026 4240 12380 247: 9507 5676 8328 9317 3732 4437 1163 9237 8320 2838 8151 1714 11146 6077 9057 11217 2449 10690 9448 10293 5728 5782 2401 4138 7730 4667 11152 2750 5910 1459 8501 967 3942 249: 5305 5158 1726 8705 7617 4366 12092 7504 11434 7904 250: 909 10291 9115 8458 1394 8188 6229 2718 3041 1813 8123 2293 4615 5989 251: 5788 3707 4166 1309 11626 1215 9592 10564 11762 2922 1120 12246 10130 6124 7520 7244 10681 11835 10359 11822 1766 2023 3987 4219 4929 3514 7009 6835 10366 252: 2506 10724 1168 12248 3861 6955 5455 8083 2472 2882 11296 7518 4531 2790 5220 4642 5764 10555 8516 7162 10500 9751 11410 3195 949 2139 9846 4335 8027 1533 9734 7365 5135 8792 10929 10357 8500 4674 5959 6248 9723 9847 2620 3874 6654 2979 2131 8267 8917 1975 1952 5318 5235 10456 6570 9295 5997 8133 9082 3101 11307 5913 10426 10488 9032 1935 11387 5730 9598 886 9453 3484 2108 9605 253: 9563 6621 3102 7854 11948 9707 2789 1234 7544 3885 709 3508 2080 8875 6633 5726 583 9480 6387 254: 2558 10259 7830 12190 11787 11233 11804 11932 5432 11382 10976 10354 8558 8784 1077 255: 663 256: 3155 8327 12074 9950 11278 1918 6688 12219 11002 11810 8671 11340 3023 2359 11271 7811 5557 10846 11839 5352 9877 1249 257: 5521 2418 9398 6286 3794 2948 10602 1167 9572 8598 4842 10051 8479 1101 2475 4960 4151 11114 7441 9907 5012 10145 5948 5536 7793 2678 1630 5607 3893 11211 4471 2407 5192 10494 9235 5625 2844 7863 1916 11840 9416 12031 7637 5138 1397 10345 11318 10309 533 5104 9566 258: 10132 11629 1984 259: 2502 2744 1758 1245 7521 1770 3621 3677 7322 6549 3343 3277 665 1392 5927 4207 3763 11133 10919 8597 7914 1260 825 4249 7390 8418 9344 1332 11207 9792 10283 8237 9052 10573 4819 5161 2192 9433 9103 11532 1235 9170 7685 12286 7576 504 9858 5613 773 12105 6580 8482 882 7672 11475 4067 260: 5500 10296 1405 4006 3542 3588 9697 3853 9860 4078 11994 5042 8840 5076 11683 7326 10026 11098 7930 10838 7510 4570 2206 6315 10542 6334 790 3761 8956 812 5842 7642 9437 1657 4261 10932 6736 7695 1678 11518 4057 11273 6908 8749 261: 7236 10747 6886 8505 4433 2828 262: 5541 12099 1314 7357 4849 6797 10245 8407 7689 11614 11634 10992 8211 9445 11122 3505 3148 7133 5137 5978 7204 6146 1059 3030 11553 4770 4028 2756 3934 2656 9282 5506 5701 12125 7721 5870 10689 11077 6742 9122 3045 11005 1242 4623 1135 12324 9419 4799 3549 860 4326 6616 12346 4982 1794 5146 4991 1988 4589 5126 3279 9035 12249 8864 1774 10361 7949 3640 1388 9286 11235 1803 6587 9401 2722 10861 1954 6421 4603 3258 6379 3220 2945 10757 6351 7391 12326 8560 1725 11541 7338 11740 2415 5573 2977 4393 1588 5712 6159 10673 7398 1137 10128 263: 5581 3054 4968 11826 7738 7209 11043 9303 8847 11344 4650 8603 6538 7278 11262 9330 1403 3746 1381 7631 8428 2483 4715 11572 10166 7872 4218 1555 9388 4651 5293 11379 7883 5692 6376 9091 11863 5991 7677 3240 9457 2300 10016 6676 7461 7839 866 4971 11657 5928 7762 6798 3314 7619 5988 2960 8922 1702 6642 2170 264: 6344 6298 1512 7511 5719 2491 5202 10321 3352 10631 5917 6083 9894 5968 3590 12458 7922 8486 265: 5263 2200 8210 4468 4206 4894 5244 2592 10185 5266 7690 5903 9738 7426 5696 649 2130 9378 2976 8828 5950 11690 877 9138 4017 6360 1056 10568 824 1530 9517 8233 3151 753 7163 5754 2049 530 8273 7202 11941 5905 6366 6487 2697 7635 6279 12035 10146 6342 752 8246 9931 692 10126 8766 5561 11222 3361 10946 5242 8076 2405 2617 1865 2657 8607 5921 6471 5322 5204 8380 9132 7500 10092 3267 8286 9969 6973 11893 12262 10563 3738 822 6392 622 10857 9505 11086 10533 2312 3827 8685 2271 6241 5008 3275 11760 7717 8735 5121 4477 10541 2457 12093 672 10642 3263 4132 3908 2158 1110 9674 4706 5371 4655 1385 7054 10162 4026 9426 798 8527 7663 9407 1548 12317 1065 6247 3991 6995 10511 3310 7942 7749 971 8054 3702 7725 4149 1430 4869 8240 863 5849 2614 676 6373 9434 6569 8422 7905 2065 8226 1508 9293 10963 7217 1061 11930 5694 4859 2066 4479 3376 3741 8660 4973 5325 12445 7501 11478 9009 266: 5282 9034 7946 3565 11010 7556 8542 2900 11813 2791 11619 8609 8565 3327 12063 10274 10374 900 7557 267: 11439 1214 4657 9436 2384 9226 4077 682 8386 4448 11550 8196 11891 5540 8891 2221 2140 6220 8049 9688 10817 268: 10697 8194 3123 9121 966 3221 3093 269: 10295 1410 8017 3948 5643 4846 6118 9778 6770 9890 12451 1151 3574 4835 270: 7653 9879 12273 7937 9112 4263 8319 5428 2874 11856 9069 3095 8815 2046 641 8043 4590 11907 9367 1159 3424 9260 11646 11305 11376 7165 4574 4181 2391 12397 5370 5450 8238 11297 271: 9887 1594 4561 739 2428 7289 3300 8694 1074 4512 12138 1956 10699 1707 7373 11092 8691 1166 9373 700 1732 4645 10654 1460 1285 1281 8288 11083 1510 2274 11977 10396 750 9084 10927 9906 5155 1382 8164 2022 3091 2406 5839 11635 5635 7282 5281 6545 9626 11931 2083 7990 5071 3039 9941 2486 6359 11986 8040 5737 7068 2386 969 8753 10709 1706 3782 5246 2968 11013 11425 6000 272: 12210 3011 273: 4502 1337 6810 4527 5021 4545 10234 4774 8930 11081 12176 4641 4805 10993 5304 3150 4398 2850 11682 10640 7643 2956 7696 10206 2017 10653 12339 11567 9175 5639 9149 4145 10829 7654 7745 6090 4474 12310 11298 4324 7989 274: 10151 1343 9690 5795 915 6283 12244 6167 12415 11244 7538 669 10236 7748 5338 8272 3603 10715 8221 6126 8746 1147 3862 1386 4626 9462 3382 11669 9745 1953 5485 11800 12029 7011 4464 3433 6878 916 10508 9362 6949 7323 9591 3126 4283 10994 4969 5567 2076 829 11238 1408 1733 8827 7859 8376 2390 6010 9864 10550 11449 4453 11559 574 12253 12301 2742 3302 7911 10899 1584 10625 907 6246 11192 840 11341 609 3764 10344 11888 4851 2989 7281 5505 764 10714 10412 3223 2713 1255 11776 10389 3325 10604 4254 6746 5745 2438 4102 3660 11358 6251 10395 7396 7923 5336 4661 5515 10273 11125 8513 6191 5873 5865 5467 3138 6058 9002 6100 3066 7028 7343 7983 11854 8332 7665 6357 8659 3544 6694 10434 1608 9976 6353 10465 5897 3342 12015 10483 2353 3379 8843 11336 899 4186 2077 11282 2511 696 3951 275: 3988 802 11542 11369 9017 11035 9816 5563 4495 3642 6836 1845 8908 5111 3844 9772 8011 11500 12331 3612 3997 1045 8865 7631 11726 9696 6732 10000 4895 3344 697 6470 807 8854 9589 10566 9152 8713 1944 7340 702 3836 8254 10886 564 1886 3831 6333 6117 1496 11477 8135 1724 950 5818 10193 8811 8628 905 3898 8299 8358 12402 4237 11838 6642 1355 276: 2169 11476 7821 9495 559 1266 9387 6032 9172 6564 5439 10117 12044 3527 12088 1802 10038 6104 11857 1112 5026 1804 1488 4647 5852 8919 3271 10791 1940 10169 5685 4328 8860 278: 4220 5703 10281 11415 5739 1519 633 8471 11602 3177 10311 3720 6857 7703 4881 8725 4607 2350 7783 8244 9074 2110 8593 11793 9543 3699 7208 9578 2215 5605 2949 10824 5027 5513 1127 2378 6061 8900 5611 1681 500 8962 2636 9653 6323 8203 279: 7977 4811 2446 5969 7781 11781 6820 3168 5194 2308 2692 7979 3206 3191 10546 3728 7408 7127 10251 8926 2683 4190 11458 624 2770 7857 12407 12231 4035 12461 9756 2575 8112 5600 5560 3284 280: 2287 7413 3795 955 7407 6771 3577 6512 918 11231 2508 9630 4279 11287 9474 7449 1585 11322 281: 2028 1786 5526 6693 4360 11647 11029 7795 3076 6567 12424 5784 8619 7640 719 10603 3255 4058 5009 9469 3104 3560 1991 4995 7473 3131 3446 11778 2436 11154 1914 3301 3697 6627 2421 2985 8765 11696 2067 2884 6975 808 4659 12259 6116 4053 3061 1241 2503 9710 8539 11176 5157 12436 5596 1069 7135 2640 3543 9315 7926 1963 11876 11825 1926 4235 2876 8700 1574 12368 12254 823 4476 3534 6997 1948 9739 4457 7074 566 5110 3289 4223 1173 11332 2668 9331 8372 3257 5631 1114 2596 9870 5609 11966 8627 4572 11263 1106 2517 282: 6885 12394 3460 5431 10471 1949 11830 8616 10537 8905 8718 7566 11255 7655 4357 9718 8693 10578 5918 7620 3719 6735 8835 7577 2545 10266 4353 2003 7606 10833 4397 5077 8739 8635 9581 9878 6257 9391 10046 9449 8224 6202 3529 7739 3053 10569 6689 9494 3892 9795 5280 4728 8773 5720 6472 6961 12395 1772 9164 9819 9351 12175 4380 8389 8062 5525 4322 6666 602 9760 6826 9359 6952 8535 1524 1587 8816 8477 6697 3154 12001 1083 3502 4513 3252 9470 1909 8651 2347 7341 8427 7945 5368 8447 2143 1516 9817 8044 7032 7719 735 4038 4756 4966 5522 6631 11853 4975 7003 6724 9360 9209 1951 12228 1609 1421 7481 6644 8777 12140 10687 283: 1264 11225 3729 5940 7731 12370 659 7066 9515 4931 2567 6128 3931 2518 6686 705 5223 5813 2082 10751 3378 10518 8119 7714 7598 8128 5904 8647 9354 8977 6953 12230 9075 10913 621 2918 6596 6500 5250 5906 3182 10854 3105 11319 10872 7611 11668 645 3083 7126 3944 10161 10805 5835 2014 5486 2092 8804 4986 1747 8661 3669 11765 3911 5170 5131 11064 4830 3169 4771 8468 2199 9730 12042 6401 3880 10156 4342 4126 12422 2433 2908 7692 4703 3001 5603 8034 9394 7102 11362 2880 7164 3841 2730 2902 7741 2688 9762 10756 1500 12018 7554 6614 4299 10031 7987 4336 3353 1452 7666 3538 7184 1032 496 4521 6170 1031 12261 7659 3522 3406 6207 3941 3107 6114 1364 7036 6553 5645 11299 1591 2260 2527 7807 10915 11381 3339 4106 3403 3513 284: 6275 8031 11396 11068 6144 6901 1677 9747 5479 10638 10458 12008 7191 4441 10503 9320 5378 6741 8310 11937 5463 5820 6201 4251 10652 5984 3650 4243 8318 2772 690 4162 2152 951 3034 11886 4131 4517 4483 1053 4076 12352 2833 2445 10815 10247 9468 1097 9265 285: 940 9000 9831 9731 7276 8668 6396 7301 2470 10278 2467 4421 7774 3286 2063 1808 2189 7260 11548 8989 1250 5911 4075 5203 2358 5558 5226 7431 1785 6448 3767 286: 2145 8599 10948 6225 11072 2197 2757 6638 5311 7645 1982 4821 1376 2555 2747 10907 3161 4905 1891 7299 6938 8788 893 11843 8470 11662 5421 2349 11864 7049 10028 1222 2608 12111 2214 1335 10383 8738 1841 6534 1246 6377 2646 4358 5942 7951 8088 4662 11432 6967 5837 3017 8907 9593 9659 482 3666 2501 3744 3064 9837 10637 6827 1996 9849 1985 2873 1882 5028 9685 11008 8686 6446 7029 7027 5458 7033 6213 6295 1076 12256 8859 12163 931 4920 11878 3715 9643 7875 8225 12038 8403 11408 6962 8291 12013 9666 7532 10425 3996 4964 10826 484 1417 6821 8311 10644 5302 7711 1979 8295 3649 12328 4085 5838 1563 2427 1369 10062 2039 3137 7986 6801 1872 9285 11018 1415 3585 6710 1520 7573 5535 12389 11651 8631 11896 1279 4516 4043 10442 4972 3363 1219 8277 6808 10460 10481 4724 4086 4843 8260 6972 8897 9573 6840 1319 4866 6354 8954 4541 9078 2367 7262 8419 4023 5593 2103 5880 9207 10480 4878 8507 4682 1189 7154 2118 3589 2629 11281 9269 9208 1812 12377 2700 6802 5328 9597 4302 10352 11089 3569 9420 11397 896 7628 6205 9287 11031 5218 11549 6524 10574 1881 5339 5045 4071 10233 10909 12281 7025 7971 11737 11915 8033 9418 8461 8346 3737 2205 2107 606 11914 3822 11576 7789 5578 5056 1764 6011 8217 12298 10433 3351 8600 1967 9809 5511 4280 10360 2531 1660 5200 1817 1484 7733 12423 10823 5112 1901 8200 8462 5319 7648 4216 12052 6554 10867 5774 3524 10230 1877 9711 9335 6059 11667 8707 11717 3197 7064 11940 10287 10939 1480 844 4796 2135 749 7963 4915 1352 6211 5892 11275 3046 4718 9194 4402 7782 6584 7550 7199 6271 10918 9995 4084 10596 8450 2859 6992 10175 8530 10138 850 9383 5116 7826 4456 2062 5628 746 6980 3618 9693 8455 4187 5821 8832 9025 9657 1017 11242 9336 9925 3739 11971 5185 288: 5348 6988 9850 7061 12393 5642 4272 7664 5768 2239 10722 11731 6181 8354 8858 4580 2292 11675 11955 3003 2309 6978 7437 6963 3348 1384 3367 4295 11024 6522 10818 2095 8059 5391 4575 2845 751 5938 2005 7757 8416 1079 9930 6064 8019 7973 5001 8966 8103 3696 8845 10877 11016 3966 11997 7483 4704 1755 5574 2153 10075 4543 613 4822 4321 1170 7459 10843 7479 4345 1028 821 7615 10064 4827 4045 9607 3901 9278 4885 8800 3708 12309 8573 4029 8098 976 11913 9490 6374 9234 892 11638 11650 842 5597 11803 9447 532 10820 6853 11295 10415 10973 6258 625 6489 4373 8623 1861 11497 10774 1341 5241 7291 11074 9223 1636 10485 8099 10704 1689 3110 1625 3479 2459 7846 4670 4908 11404 7790 11959 2302 4099 7169 2704 3935 5659 11109 1971 4882 1420 2724 7516 2619 11145 726 11950 10404 11066 8602 4952 4595 8430 7957 6667 4098 5760 3721 289: 1683 12362 9113 4392 7600 2414 2717 7366 11744 2316 12432 10453 11679 8722 6948 2664 778 5462 5825 6919 945 2473 6807 8373 2166 1633 7234 7776 12372 290: 4700 7981 9048 2079 2356 10812 9843 3864 2142 9836 1057 3447 1172 7866 7140 8426 5441 8679 8292 7107 1826 4121 10814 1141 291: 7236 8505 4433 293: 6920 2766 12174 5078 10056 1978 3146 3915 7250 6194 7842 3385 12026 10851 9549 5924 9689 7070 3010 1015 3080 294: 11118 1686 1569 7161 9314 6479 5327 8152 7604 2735 6160 11023 6082 7438 11324 658 6632 295: 1797 12327 9056 1769 8521 6141 4451 10662 3121 6729 4002 296: 11665 4628 8100 11272 2962 6690 8757 3907 736 10968 8396 4139 2701 2537 11009 3140 569 636 10430 11348 11239 4423 8170 297: 10040 6879 1716 4274 5840 11946 10045 1299 4204 6868 1203 1570 12187 4055 11034 11867 10121 8764 9896 4383 10441 11603 5197 7751 2307 4538 8156 9640 9117 9173 2889 2739 1302 11224 6739 12406 5005 2175 11240 6051 8920 4088 2602 3670 4411 2277 8695 9684 2157 9102 12411 667 11355 12131 3377 4744 1665 1819 9771 6610 3356 8252 7484 12046 2109 6629 7975 3550 12082 11922 2488 7468 6702 3819 12435 3037 7503 8208 2368 1656 10950 7799 3709 11821 6754 9570 3461 2514 10798 6302 9565 12201 1206 7542 7345 9166 1827 298: 8139 8641 6523 7360 10848 7080 11351 10710 6316 8361 9946 1907 6719 10272 12085 7644 8212 1763 299: 6133 301: 2843 8911 6094 12023 11991 12055 2010 302: 10750 3288 4820 10759 7232 1468 2951 4205 1048 303: 7006 9229 1705 10858 4364 880 1760 7465 4675 12426 5360 2156 9318 8825 11203 6042 7668 11101 1703 6193 7506 6825 5555 4308 304: 1683 4392 7600 2710 7988 10089 2414 2717 7366 2316 960 1455 10749 9333 4153 10429 6807 8373 305: 6095 6918 10432 6852 5239 3438 10943 9551 695 9080 5993 306: 4430 2094 4292 12439 307: 1536 9023 11880 10936 7226 9524 9199 6926 6112 11618 7321 8750 11623 4860 6588 5722 8796 4694 11392 7090 10582 308: 5238 3842 10493 3617 12025 10781 7017 10148 4213 1647 734 1922 1286 6020 11398 4553 4130 1328 10923 2987 997 9857 1651 8745 1276 11827 5769 11903 1711 10772 2601 8974 5893 9389 3765 6869 1320 8841 560 4916 9060 7308 3672 10804 7998 5884 7476 6162 309: 8801 3541 1041 6711 7964 681 876 1839 9861 3546 9830 9865 1265 6813 11471 9210 1347 9892 9273 7114 12376 2419 3964 310: 4125 2643 777 875 8914 5741 7486 11181 7454 10520 1438 12303 9051 5051 7954 6123 3280 1495 3158 3837 12409 4690 2998 8519 7534 797 9155 2452 10780 10529 1310 9092 6012 8983 10985 4080 2765 2516 2971 5804 7794 9472 4925 1082 1535 8326 10677 4469 10965 4601 5747 1947 11884 8621 2712 485 497 5002 7211 5018 4902 11085 5772 3149 11134 3570 7109 545 2244 5163 4170 10310 2612 1373 10624 1896 11243 584 5259 3993 4281 1326 8302 4033 3299 1465 9045 1664 311: 5122 8544 1850 3407 3082 2101 8807 1743 4416 4485 4518 3943 4757 7512 786 9889 3591 2580 2002 3092 5789 9825 994 3209 8435 4537 11593 7021 8789 10106 1573 6780 7096 6073 7736 7171 4282 4394 1849 930 972 2847 1117 8721 7189 2100 5149 7221 11953 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4018 4039 11441 9737 9811 643 4090 4666 4546 6461 2864 1198 10505 1414 8510 1332 9632 6508 9748 5207 7702 3747 12087 3357 9406 3417 4104 3657 3772 11104 8237 8514 8436 2571 4116 3922 8122 6209 10639 693 732 4062 7892 686 3094 3499 3000 2167 6655 1509 10401 1427 1579 2802 9356 8013 6206 3904 7261 9433 934 510 6382 8330 9157 10376 9699 832 1479 7796 2553 7440 3791 1738 5177 7444 12266 3261 1236 5344 3157 5577 4289 9028 2374 9986 4510 5313 12252 4434 9805 4625 2489 1554 2057 8415 7724 6950 3790 10071 1888 10647 2936 9844 6590 642 5953 9569 11882 6358 2897 2797 5667 3259 1008 2009 9475 11260 1252 8074 3306 4480 6785 10892 7801 2478 12060 10181 10457 11313 11251 10961 5398 11091 1021 8867 11189 2479 1526 2174 11424 6658 4950 11613 12337 2055 4096 11784 5724 6115 11058 9979 6460 5035 6730 4923 6381 6683 3081 6021 11093 12172 6580 7672 6698 439: 9050 1624 11490 9137 4683 1472 11419 11201 12153 11407 2333 8918 12149 10769 2801 9090 6033 5211 11474 12365 5630 12100 6330 2526 2036 440: 5951 3216 9673 4696 9814 3530 10953 5785 720 6518 1693 11588 10246 7120 5040 10911 11834 8071 11378 3196 5717 9753 5644 441: 7707 8538 2341 7194 5074 5690 2147 2538 9725 10428 4880 5920 10970 6335 7744 8342 11672 5446 6675 8117 1618 6922 6664 1708 10501 3809 2321 1477 3404 8823 5288 1911 4926 442: 11879 6492 3887 756 4733 6158 1728 5673 5481 11069 12381 1890 1649 2930 2784 6431 1020 3078 9576 3232 7334 2622 4189 8439 3249 3593 4179 4841 5713 12338 10718 6823 6695 3315 6663 443: 2994 605 1631 6296 1844 11844 3084 9395 1933 8702 7786 11988 2128 10660 5251 6665 7785 5248 9981 11142 4174 3452 3303 12156 4698 12118 2699 12096 7773 10611 2953 5956 12178 12170 5672 9916 7788 4953 11739 4556 6260 11846 3109 8488 8674 9574 8624 3734 11566 444: 11436 9600 4036 2771 1190 6072 6982 2138 5753 5102 4767 7415 9797 5570 7192 1387 4343 2370 5680 10618 5872 3634 11291 10696 1986 9618 10628 10894 1404 5877 9827 6200 1273 9615 2105 6034 10168 4940 1734 8417 8948 3019 8808 445: 5898 11158 5363 4614 479 7670 4772 679 6014 3641 11608 11120 8644 8810 9334 12142 6025 10895 5777 923 11900 9914 580 1904 3473 8157 9546 10735 1346 4635 12408 5326 10987 4765 12292 2408 3705 11060 920 10127 11506 11960 6468 2264 2469 7344 5771 9604 2225 2423 5614 6255 4052 3890 5154 4753 2006 4144 913 1893 11578 1641 10844 7418 4406 8743 3664 7010 6263 9188 8333 11184 3586 7119 4592 10897 1543 4041 3967 10446 6161 8214 9019 8506 8178 8166 2609 6272 11990 10220 10720 4720 1372 8999 5687 1064 2764 7876 2726 10484 8618 8445 878 11391 5389 1532 4482 2194 5970 2854 1329 5025 8114 12116 540 8209 6786 1605 3796 9500 6774 2846 6204 7569 9752 3423 2248 2665 8972 12410 8446 3821 8648 9439 6312 733 11327 2605 8876 10319 7537 5908 4987 9013 3443 9602 12276 7661 1274 10200 5396 11003 10042 11749 8121 11076 9974 11026 1419 10891 1463 5977 2460 6881 10165 3756 2451 5549 1517 2237 9215 4893 6903 10551 603 8871 3933 7551 7660 6459 2448 10902 11799 12162 11708 5866 3938 11582 5019 9219 1223 2361 3750 10152 5770 8615 4412 7727 1552 5097 10590 6782 9346 10110 8347 1399 4798 8063 10203 7369 3212 3929 4222 2932 2814 2808 4003 6572 10580 7424 7144 10581 8029 614 12041 9422 11418 7355 4890 9654 3858 6591 526 446: 2763 11630 10646 5423 8132 999 1338 3592 12392 1695 1880 447: 5756 4298 9204 3118 7348 2187 6044 11528 3135 8988 3176 11446 4858 5386 6613 449: 12062 3366 9305 2281 4123 4637 8367 769 2719 4653 1084 7458 450: 12147 9257 3555 5006 5380 3990 699 7196 8444 1317 486 5669 9008 10806 1852 3245 1913 451: 7961 6784 10385 12354 865 6268 12456 4879 11331 1843 3415 3457 8727 9428 4065 1063 1920 845 10276 6165 12385 11052 4847 4310 4673 2038 4649 9641 2122 7093 11894 3047 6855 561 8107 4273 7069 9794 9178 12356 1917 6681 10830 10176 11333 7035 11763 2291 9680 10796 6237 2745 8942 1107 5551 2354 8913 5062 2272 10205 6966 8747 11111 5876 5902 9949 12045 452: 6394 10174 11264 2929 1796 12463 7434 9390 4194 2477 11245 3690 1838 5530 1929 9136 7237 989 11473 6317 11703 7760 2499 9922 7259 6310 2561 2364 10199 11466 796 453: 6394 10174 11264 2929 1796 12463 9390 7434 4194 2477 11245 5530 1838 1929 7237 989 7421 9348 1044 4048 10219 9509 8398 5286 5871 11487 980 7210 816 796 454: 6625 1795 11957 10600 4695 8786 1854 826 8093 5089 8783 5261 542 6979 12146 11354 11208 4567 3736 3070 3227 2154 7613 9181 2375 7852 10957 10358 4616 8853 2165 455: 11314 10125 5372 1221 9486 8375 5654 7809 1768 3229 4762 10599 4701 456: 8762 11259 9107 10327 1525 10723 11286 8082 8795 7526 1751 9617 6173 10210 8996 5165 9994 10981 2651 8924 5646 10734 1043 6503 7160 674 10942 6208 2500 2232 5435 8003 7775 7197 11386 9614 7336 4389 1201 457: 6933 2534 5034 10920 4668 801 7463 9241 4122 10093 8480 1669 4875 458: 12340 917 2331 6174 4354 1998 5058 11006 9105 6744 12417 3551 10011 2512 3369 459: 1750 2582 939 7800 4167 10863 1778 3187 3119 8688 9519 7715 3465 8518 7218 3654 9851 3214 9839 8754 11131 3785 10516 5456 1066 9161 2498 7968 4449 8957 11214 11622 11993 12161 460: 3393 11215 6311 8704 11428 12454 7996 9854 1062 3012 10737 12145 4242 461: 1596 11261 12367 6847 9799 1697 3584 4419 462: 2559 3211 8719 9526 912 8678 9169 529 7339 463: 8985 11453 9101 1592 996 9514 8633 664 10466 11427 8230 2310 3910 4193 2788 12130 1565 10560 8540 6384 11084 4965 9345 1623 3579 12441 9119 1042 3490 8581 6214 7907 464: 5490 9114 10657 1047 9324 2641 3532 465: 5468 6657 4173 4351 1080 4899 8973 2817 10047 7847 1370 2389 11692 10139 7089 6369 5848 9153 2447 6533 10312 3428 12166 7229 12336 1718 4369 11599 3520 1903 12300 1482 466: 1224 5723 2541 11729 5963 4598 5738 2220 8201 5996 11234 5067 943 2089 10322 467: 11200 7567 3580 4845 2181 10852 549 2202 11686 1089 7836 9898 1118 4587 4761 11028 7798 9104 8548 7649 5889 1358 3846 12287 10700 8601 5442 2137 10267 7042 2634 760 1406 9108 5922 3789 6004 4198 10766 2454 3807 12306 12290 11237 9088 7917 9288 7212 11361 1586 3575 1993 5292 10350 12258 2782 5845 8104 4936 9246 10103 7474 1873 6809 9171 12400 6038 9410 2560 5403 2736 8012 1197 1859 4317 1762 11062 1788 1589 8632 12112 7865 2796 10617 1478 3978 7405 8958 12158 4314 1096 3383 6169 469: 6501 9978 9506 8048 6041 11554 7940 1311 761 9444 1675 9956 8980 3509 8369 7051 10464 4793 9243 11137 9702 650 2162 2318 8547 5167 2224 3189 11426 11921 12073 5571 10065 11294 1231 1534 12094 1787 5994 2871 3170 9945 1211 6776 5232 9755 3346 4529 7769 10952 2907 4108 1825 8189 9705 2337 5815 6517 2024 9712 7508 10391 12009 7433 2870 5210 5086 1723 1765 470: 5084 11194 9575 8315 3179 1987 11812 3976 3760 2762 779 4164 11691 10789 12264 5656 10659 2104 11167 8323 4400 10935 5221 5623 921 3463 10656 10670 4215 5379 2522 6418 982 7059 3322 7858 9733 8620 6578 6976 10694 5052 2725 5937 3180 5594 11700 8684 4226 10509 12384 11783 11615 3194 8836 3058 4838 1075 589 6318 12032 4746 6787 9636 2112 12444 5488 10076 9098 4011 2926 4776 8892 12036 1627 1229 7868 12227 4806 3425 3106 5517 5569 2805 6222 1072 3265 7386 6709 4420 8943 8561 11384 4492 6943 7513 5489 11412 5620 935 4602 3992 12126 4524 5295 471: 4125 2643 8914 5741 7486 11181 7454 1438 9051 5051 7954 6066 1495 10258 12409 2931 2998 7574 8519 10264 7534 797 3773 10985 4080 10803 2516 7845 10965 4601 5002 7211 11852 3999 6602 11085 5772 3149 11134 10624 1896 11243 5259 3993 4281 1326 4033 3299 1465 9045 473: 1243 1128 2040 10378 8222 10746 10012 7467 5079 1528 11934 8515 474: 6601 527 2379 10196 6137 8682 4571 5965 1720 11962 7324 6890 2000 3989 9528 2837 979 1830 4658 5140 12206 7572 11257 3730 3247 9845 5430 6818 11818 9582 1443 9531 2032 12196 8459 12235 1905 7764 7158 3049 7860 6184 10022 5125 11754 776 11248 1635 11123 3134 3576 12200 1437 2294 10118 5180 4802 2992 6519 5231 2482 11465 7884 2815 6520 12103 10061 758 8634 12134 2903 10025 5634 5303 4014 11481 2853 4147 5919 1025 8579 11370 10373 9451 7816 8473 6909 2056 1942 5495 9556 941 11202 3129 11586 7180 4318 8652 1094 12057 8148 3547 1039 1685 7743 3838 11056 11872 3487 6540 4865 2136 12002 1735 7894 5527 9635 6171 3419 11976 11116 4202 2787 3857 11185 8493 7897 9631 2132 5397 11537 4725 9882 10003 7886 11920 8820 1566 8009 6859 5036 1810 6339 5982 10204 6829 5887 11503 1164 4505 10947 7478 11732 2729 11967 6906 1181 12106 7401 8306 4315 3213 2969 11177 10260 11850 5333 4769 3231 10237 11065 11935 2196 9700 8932 1776 4348 10232 2954 9540 9284 6427 11488 1448 5878 4288 11911 1606 5899 2216 4930 828 8456 8300 12173 1581 3969 3308 3733 8146 4107 318 318 10810 10688 7258 3755 6413 3072 2938 1958 2013 3222 7116 9552 6743 3633 5410 10967 9652 3051 4884 6438 2195 3521 715 11816 5080 6811 11824 6148 7701 2120 2012 10779 7038 2714 1004 8131 3368 8676 2320 7910 10733 11153 5976 2606 1254 10261 10527 6399 7022 2373 12098 10524 11061 2677 2819 8155 8898 4897 3568 2061 2343 4454 5367 5900 8137 9016 5191 9012 754 8169 1230 4040 9541 8193 5427 7697 3237 10536 3816 7388 5399 11230 4472 3241 2168 4442 3086 3186 1691 2369 9347 4435 6197 475: 2644 476: 12084 6235 4759 10347 8520 3926 9058 7491 1621 477: 12177 6814 4681 6355 5964 1174 7480 2252 11814 11423 4309 10760 10292 8167 9787 1400 10173 5931 4566 772 6147 5362 2160 478: 8803 12320 5017 819 1756 7073 10263 8731 3488 5675 2434 11042 2673 2990 11910 11377 1682 12429 12056 4814 742 2402 12165 7948 11221 10036 10314 10977 4596 1323 10078 7929 3624 6883 3114 10477 3389 8708 5663 6480 3774 3454 9482 11666 5598 6307 9709 5580 4619 5929 3207 12379 6931 5030 938 7247 12101 7031 4907 11965 10984 6905 6496 673 2777 5113 1378 10218 1124 4266 12160 10249 6752 4932 11395 11015 5999 10641 6043 1035 12446 4184 9645 10931 3873 12330 5943 5657 6916 7389 2698 3762 12075 9802 12250 5548 6053 6457 11456 1634 12220 4794 8173 4037 6420 926 7361 2588 7618 11802 10825 10443 7699 1560 11556 1176 8791 7303 9298 2851 9247 11674 2279 8498 4791 8531 6303 635 1977 9577 5776 8512 10792 7667 9612 3405 4341 7959 10860 3622 6528 8313 7205 4064 9631 9594 968 10331 7018 

1. Transgenic seed for a crop, wherein the genome of said transgenic seed comprises trait-improving recombinant DNA for expressing a bacterial phytochrome protein.
 2. Transgenic seed according to claim 1, wherein said protein provides improved tolerance to cold stress, improved tolerance to water deficit stress, improved tolerance to reduced nitrogen availability stress or increased yield. 3-4. (canceled)
 5. A transgenic seed of claim wherein said DNA is derived from a Pseudomonas florescens.
 6. (canceled)
 7. Transgenic seed according to claim 1, wherein (a) said crop is susceptible to a yield-limiting environment; and (b) transgenic plants grown from said transgenic seed of claim 1 thrive in said yield-limiting environment.
 8. Transgenic seed according to claim 7, wherein said yield-limiting environment is cold stress, water deficit stress or nitrogen availability stress. 9-12. (canceled)
 13. Transgenic seed for a crop, wherein the genome of said transgenic seed comprises trait-improving recombinant DNA from a gene for a protein having amino acid sequence with at least 90% identity to a consensus amino acid sequence in the group consisting of a consensus amino acid sequence for SEQ ID NO: 240 and homologs thereof through a consensus amino acid sequence for SEQ ID NO: 478 and homologs thereof, but excluding SEQ ID NO:391 and homologs thereof.
 14. Transgenic seed according to claim 13, wherein said protein has an amino acid sequence selected from the group consisting of SEQ ID NO: 240 through SEQ ID NO: 390, SEQ ID NO: 392 through SEQ ID NO:
 478. 15. Transgenic seed according to claim 13, wherein said recombinant DNA is used to produce said protein.
 16. Transgenic seed according to claim 13, wherein said recombinant DNA is used to suppress the level of an endogenous protein.
 17. Transgenic seed according to claim 13, wherein (a) said protein has the function of a specific protein that has been demonstrated in a model plant with efficacy for an improved trait as compared to a plant without said recombinant DNA wherein said specific protein and trait, are as indicated in Table 5; and (b) transgenic plants grown from said transgenic seed exhibit said improved trait
 18. Transgenic seed according to claim 15, wherein said protein provides the trait indicated in Table 5 for a model plant-expressed protein which has an amino acid sequence which was used with homologs to build said consensus amino acid sequence and wherein transgenic plants grown from said transgenic seed exhibit an improved trait which was demonstrated in the model plant expressing said model plant-expressed protein
 19. Transgenic seed according to claim 13, wherein transgenic plants grown from said seed exhibit increased yield as compared to similar plants without the recombinant DNA.
 20. Transgenic seed according to claim 13, wherein (a) said crop is susceptible to a yield-limiting environment; and (b) transgenic plants grown from said transgenic seed thrive in said yield-limiting environment.
 21. Transgenic seed according to claim 20, wherein (a) transgenic plants grown from said seed exhibit increased yield as compared to similar plants without the recombinant DNA when said plants are grown in a yield-limiting environment of water deficit stress and said protein has the function of the protein with an amino acid sequence selected from the group consisting of SEQ ID NO: 268 through 294, 298, 345 through 357, 359, 367 through 369, 374, 398 through 424, 435, 439, 463 through 478, and homologs thereof; (b) transgenic plants grown from said seed exhibit increased yield as compared to similar plants without the recombinant DNA when said plants are grown in a yield-limiting environment of heat stress and said protein has the function of the protein with an amino acid sequence selected from the group consisting of SEQ ID NO: 268 through 294, 298, 347, 359, 367-369, 435, and homologs thereof. (c) transgenic plants grown from said seed exhibit increased yield as compared to similar plants without the recombinant DNA when said plants are grown in a yield-limiting environment of high salinity stress and said protein has the function of the protein with an amino acid sequence selected from the group consisting of SEQ ID NO: 298, 424, 439, 463 through 478, and homologs thereof; (d) transgenic plants grown from said seed exhibit increased yield as compared to similar plants without the recombinant DNA when said plants are grown in a yield-limiting environment of cold stress and said protein has the function of the protein with an amino acid sequence selected from the group consisting of SEQ ID NO: 240 through 267, 276, 277, 298, 346, 366, 367, 434, and homologs thereof; (e) transgenic plants grown from said seed exhibit increased yield as compared to similar plants without the recombinant DNA when said plants are grown in a yield-limiting environment of reduced nitrogen availability stress and said protein has the function of the protein with amino acid sequence of SEQ ID NO: 315 through 344, 364, 370 through 373, 438, and homologs thereof; (f) transgenic plants grown from said seed exhibit increased yield as compared to similar plants without the recombinant DNA when said plants are grown in a yield-limiting environment of shade stress and said protein has the function of the protein with an amino acid sequence selected from the group consisting of SEQ ID NO: 295 through 314, 370, 427, 436, 437, and homologs thereof.
 22. A recombinant DNA construct comprising a promoter functional in a plant cell operably linked to trait-improving recombinant DNA from gene for a protein having an amino acid sequence with at least 90% identity to a consensus amino acid sequence in the group consisting of a consensus amino acid sequence for SEQ ID NO: 240 and homologs thereof through a consensus amino acid sequence for SEQ ID NO: 478 and homologs thereof, but excluding SEQ ID NO:391 and homologs thereof. 23-25. (canceled)
 26. A method of facilitating production of a crop comprising providing to a grower of said crop transgenic seed of claim
 13. 27. A method according to claim 26, wherein transgenic plants grown from said seed exhibit increased yield as compared to similar plants without the recombinant DNA.
 28. A method according to claim 26, wherein (a) said crop is susceptible to a yield-limiting environment; and (b) transgenic plants grown from said transgenic seed thrive in said yield-limiting environment.
 29. A method according to claim 28, wherein (a) transgenic plants grown from said seed exhibit increased yield as compared to similar plants without the recombinant DNA when said plants are grown in a yield-limiting environment of water deficit stress and said protein has the function of the protein with an amino acid sequence selected from the group consisting of SEQ ID NO: 268 through 294, 298, 345 through 357, 359, 367 through 369, 374, 398 through 424, 435, 439, 463 through 478, and homologs thereof; (b) transgenic plants grown from said seed exhibit increased yield as compared to similar plants without the recombinant DNA when said plants are grown in a yield-limiting environment heat stress and said protein has the function of the protein with an amino acid sequence selected from the group consisting of SEQ ID NO: 268 through 294, 298, 347, 359, 367 through 369, 435, and homologs thereof; (c) transgenic plants grown from said seed exhibit increased yield as compared to similar plants without the recombinant DNA when said plants are grown in a yield-limiting environment of high salinity stress and said protein has the function of the protein with an amino acid sequence selected from the group consisting of SEQ ID NO: 298, 424, 439, 463 through 478, and homologs thereof; (d) transgenic plants grown from said seed exhibit increased yield as compared to similar plants without the recombinant DNA when said plants are grown in a yield-limiting environment of cold stress and said protein has the function of the protein with an amino acid sequence selected from the group consisting of SEQ ID NO: 240 through 267, 276, 277, 298, 346, 366, 367, 434 and homologs thereof; (e) transgenic plants grown from said seed exhibit increased yield as compared to similar plants without the recombinant DNA when said plants are grown in a yield-limiting environment of reduced nitrogen availability stress and said protein has the function of the protein with amino acid sequence of SEQ ID NO: 315 through 344, 364, 370 through 373, 438 and homologs thereof; (f) transgenic plants grown from said seed exhibit increased yield as compared to similar plants without the recombinant DNA when said plants are grown in a yield-limiting environment of shade stress and said protein has the function of the protein with an amino acid sequence selected from the group consisting of SEQ ID NO: 295 through 314, 370, 427, 436, 437 and homologs thereof. 